U.S. patent application number 11/493608 was filed with the patent office on 2006-12-28 for human sef isoforms and methods of using same for cancer diagnosis and gene therapy.
This patent application is currently assigned to Technion Research & Development Foundation Ltd.. Invention is credited to Dina Ron.
Application Number | 20060293240 11/493608 |
Document ID | / |
Family ID | 46324836 |
Filed Date | 2006-12-28 |
United States Patent
Application |
20060293240 |
Kind Code |
A1 |
Ron; Dina |
December 28, 2006 |
Human Sef isoforms and methods of using same for cancer diagnosis
and gene therapy
Abstract
A method and pharmaceutical compositions useful for inhibiting
the growth of solid tumors are provided. Specifically, the method
is effected by administering to a subject in need thereof an agent
capable of upregulating the expression level and/or activity of at
least a functional portion of Sef, wherein the functional portion
being capable of inhibiting RTK-mediated cell proliferation. Also
provided are methods and kits for diagnosing and staging of cancer
by detecting the expression level of hSef in a tissue sample,
wherein a decrease in hSef expression level is indicative of
cancer.
Inventors: |
Ron; Dina; (Kiryat-Tivon,
IL) |
Correspondence
Address: |
Martin D. Moynihan;PRTSI, Inc.
P.O. Box 16446
Arlington
VA
22215
US
|
Assignee: |
Technion Research & Development
Foundation Ltd.
|
Family ID: |
46324836 |
Appl. No.: |
11/493608 |
Filed: |
July 27, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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10963439 |
Oct 11, 2004 |
|
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11493608 |
Jul 27, 2006 |
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Current U.S.
Class: |
514/440 ;
514/19.4; 514/19.5; 514/44R; 514/5.9; 514/8.1; 514/8.2; 514/8.4;
514/9.1; 514/9.6 |
Current CPC
Class: |
A61P 35/00 20180101;
C07K 14/705 20130101; A61K 38/1825 20130101; C07K 2319/41 20130101;
A61K 38/1709 20130101; C07K 14/4703 20130101; C07K 2319/21
20130101 |
Class at
Publication: |
514/012 ;
514/044 |
International
Class: |
A61K 38/17 20060101
A61K038/17; A61K 48/00 20060101 A61K048/00 |
Claims
1. A method of inhibiting a growth of a solid tumor in a subject,
the method comprising administering to the subject an agent capable
of upregulating the expression level and/or activity of at least a
functional portion of Sef, said at least a functional portion of
Sef being capable of inhibiting RTK-mediated cell proliferation,
wherein the agent inhibits the growth of the solid tumor in the
subject.
2. The method of claim 1, wherein said RTK-mediated cell
proliferation is ligand independent.
3. The method of claim 1, wherein said RTK-mediated cell
proliferation is ligand-induced.
4. The method of claim 1, wherein said at least a functional
portion of Sef is a polypeptide as set forth by SEQ ID NO:6.
5. The method of claim 1, wherein said at least a functional
portion of Sef is a polypeptide comprising amino acids 1-10,
267-707 and/or 288-707 of SEQ ID NO:6.
6. The method of claim 1, wherein said upregulating is effected by
at least one approach selected from the group consisting of: (a)
expressing in cells of the subject an exogenous polynucleotide
encoding at least a functional portion of Sef; (b) increasing
expression of endogenous Sef in cells of the subject; (c)
increasing endogenous Sef activity in cells of the subject; and (d)
introducing an exogenous peptide and/or exogenous polypeptide
including at least a functional portion of Sef to the subject.
7. The method of claim 6, wherein said exogenous polynucleotide is
a nucleic acid construct comprising a polynucleotide at least 90%
identical to the polynucleotide sequence set forth in SEQ ID
NO:4.
8. The method of claim 6, wherein said exogenous polynucleotide is
a nucleic acid construct comprising a polynucleotide selected from
the group consisting of SEQ ID NOs:4, 8, and 9.
9. The method of claim 7, wherein said nucleic acid construct
further comprises a promoter capable of directing an expression of
said polynucleotide in said cells of the subject.
10. The method of claim 9, wherein said promoter is selected from
the group consisting of Cytomegalovirus (CMV) promoter, simian
virus (SV)-40 early promoter, SV-40 late promoter, metallothionein
promoter, murine mammary tumor virus promoter, Rous sarcoma virus
(RSV) promoter, and polyhedrin promoter.
11. The method of claim 6, wherein said Sef is a polypeptide at
least 90% homologous to a polypeptide set forth by SEQ ID NO:6.
12. The method of claim 6, wherein said Sef is a polypeptide set
forth by SEQ ID NO:6.
13. The method of claim 1, wherein said solid tumor is selected
from the group consisting of ovarian carcinoma, pancreatic cancer,
breast cancer, endometrial carcinoma, brain tumor, adrenal
carcinoma, pituitary cancer, thyroid carcinoma, tonsillar
carcinoma, spleen cancer, adenoids cancer, kidney cancer, liver
cancer, testis cancer, bladder cancer, colon cancer, prostate
cancer, bile duct, lung cancer, and stomach cancer.
14. The method of claim 3, wherein said ligand is selected from the
group consisting of FGF, PDGF, VEGF, NGF, insulin, and EGF.
15. The method of claim 1, wherein said RTK-mediated cell
proliferation is effected by inhibition of activated Erk1/2
(P-Erk1/2) within said cells.
16. A pharmaceutical composition useful for inhibiting a growth of
a solid tumor in a subject comprising, as an active ingredient, an
agent capable of upregulating the expression level and/or activity
of at least a functional portion of Sef, said at least a functional
portion of Sef being capable of inhibiting RTK-mediated cell
proliferation, and a pharmaceutically acceptable carrier.
17. The pharmaceutical composition of claim 16, wherein said
RTK-mediated cell proliferation is ligand independent.
18. The pharmaceutical composition of claim 16, wherein said
RTK-mediated cell proliferation is ligand-induced.
19. The pharmaceutical composition of claim 16, wherein said at
least a functional portion of Sef is a polypeptide as set forth by
SEQ ID NO:6.
20. The pharmaceutical composition of claim 16, wherein said at
least a functional portion of Sef is a polypeptide comprising amino
acids 1-10, 267-707 and/or 288-707 of SEQ ID NO:6.
21. The pharmaceutical composition of claim 16, wherein said
upregulating is effected by at least one approach selected from the
group consisting of: (a) expressing in cells of the subject an
exogenous polynucleotide encoding at least a functional portion of
Sef; (b) increasing expression of endogenous Sef in cells of the
subject; (c) increasing endogenous Sef activity in cells of the
subject; and (d) introducing an exogenous peptide and/or exogenous
polypeptide including at least a functional portion of Sef to the
subject.
22. The pharmaceutical composition of claim 21, wherein said
exogenous polynucleotide is a nucleic acid construct comprising a
polynucleotide at least 90% identical to the polynucleotide
sequence set forth in SEQ ID NO:4.
23. The pharmaceutical composition of claim 21, wherein said
exogenous polynucleotide is a nucleic acid construct comprising a
polynucleotide selected from the group consisting of SEQ ID NOs:4,
8, and 9.
24. The pharmaceutical composition of claim 22, wherein said
nucleic acid construct further comprises a promoter capable of
directing an expression of said polynucleotide in said cells of the
subject.
25. The pharmaceutical composition of claim 24, wherein said
promoter is selected from the group consisting of Cytomegalovirus
(CMV) promoter, simian virus (SV)-40 early promoter, SV-40 late
promoter, metallothionein promoter, murine mammary tumor virus
promoter, Rous sarcoma virus (RSV) promoter, and polyhedrin
promoter.
26. The pharmaceutical composition of claim 21, wherein said Sef is
a polypeptide at least 90% homologous (identical+similar) to a
polypeptide set forth by SEQ ID NO:6.
27. The pharmaceutical composition of claim 21, wherein said Sef is
a polypeptide set forth by SEQ ID NO:6.
28. The pharmaceutical composition of claim 16, wherein said solid
tumor is selected from the group consisting of ovarian carcinoma,
pancreatic cancer, breast cancer, endometrial carcinoma, brain
tumor, adrenal carcinoma, pituitary cancer, thyroid carcinoma,
tonsillar carcinoma, spleen cancer, adenoids cancer, kidney cancer,
liver cancer, testis cancer, bladder cancer, colon cancer, prostate
cancer, bile duct, lung cancer, and stomach cancer.
29. The pharmaceutical composition of claim 18, wherein said ligand
is selected from the group consisting of FGF, PDGF, VEGF, NGF,
insulin and EGF.
30. The pharmaceutical composition of claim 15, wherein said
RTK-mediated cell proliferation is effected by inhibition of
activated Erk1/2 (P-Erk1/2) within said cells.
31. A method of diagnosing cancer in a subject in need thereof, the
method comprising detecting in a tissue sample of the subject an
expression level of Sef, wherein a decrease in said expression
level of said Sef compared to said expression level of said Sef in
an unaffected tissue is indicative of the cancer, thereby
diagnosing the cancer in the subject in need thereof.
32. The method of claim 31, wherein said cancer is a solid
tumor.
33. The method of claim 32, wherein said solid tumor is selected
from the group consisting of breast cancer, ovarian cancer, thyroid
carcinoma and prostate cancer.
34. The method of claim 31, wherein said Sef is a nucleic acid
sequence of Sef.
35. The method of claim 31, wherein said Sef is an amino acid
sequence of Sef.
36. The method of claim 34, wherein said detecting is effected by
an RNA detection method.
37. The method of claim 35, wherein said detecting is effected by a
protein detection method
38. The method of claim 36, wherein said RNA detection method is
selected from the group consisting of RNA in situ hybridization,
RT-PCR, in situ RT-PCR and Northern blot analysis.
39. The method of claim 37, wherein said protein detection method
is selected from the group consisting of ELISA, Western blot,
immunofluorescence and immunohistochemical analysis.
40. The method of claim 32, wherein said solid tumor is a primary
solid tumor.
41. The method of claim 32, wherein said Sef is Sef-a and whereas
said solid tumor is breast cancer or ovarian cancer.
42. The method of claim 32, wherein said Sef is Sef-b and whereas
said solid tumor is thyroid carcinoma.
43. The method of claim 32, further comprising determining a
malignancy of said solid tumor.
44. A kit for diagnosing cancer in a subject in need thereof, the
kit comprising a reagent for detecting an expression level of Sef,
wherein a decrease in said expression level of said Sef compared to
said expression level of said Sef in an unaffected tissue is
indicative of the cancer.
45. The kit of claim 44, wherein said cancer is a solid tumor.
46. The kit of claim 45, wherein said solid tumor is selected from
the group consisting of breast cancer, ovarian cancer, thyroid
carcinoma and prostate cancer.
47. The kit of claim 44, wherein said Sef is a nucleic acid
sequence of Sef.
48. The kit of claim 44, wherein said Sef is an amino acid sequence
of Sef.
49. The kit of claim 47, wherein said reagent is utilized for an
RNA detection method.
50. The kit of claim 48, wherein said reagent is utilized in a
protein detection method
51. The kit of claim 49, wherein said RNA detection method is
selected from the group consisting of RNA in situ hybridization,
RT-PCR, in situ RT-PCR and Northern blot analysis.
52. The kit of claim 50, wherein said protein detection method is
selected from the group consisting of ELISA, Western blot,
immunofluorescence and immunohistochemical analysis.
53. The kit of claim 49, wherein said reagent is an isolated
nucleic acid sequence complementary to said Sef nucleic acid
sequence.
54. The kit of claim 50, wherein said reagent is an antibody or
antibody fragment which comprises an antigen recognition region
capable of specifically binding said Sef amino acid sequence.
Description
RELATED APPLICATIONS
[0001] This Application is a Continuation-In-Part (CIP) of U.S.
patent application Ser. No. 10/963,439, filed on Oct. 11, 2004, the
contents of which are incorporated herein by reference.
FIELD AND BACKGROUND OF THE INVENTION
[0002] The present invention relates to polypeptides and
polynucleotides expressing the human Sef b-d isoforms (hSefb-d),
and more particularly, to the use of such isoforms in the
inhibition of uncontrolled malignant proliferation of solid
tumors.
[0003] Solid tumors account for the majority of human tumors and
among them, carcinomas of an epithelial origin, account for over
80%. Conventional therapies for solid tumors involves the
administration of anti-tumor drugs such as thymidylate synthase
inhibitors (e.g., 5-fluorouracil; Rose MG e t al., 2002; Clin
Colorectal Cancer. 1: 220-9), nucleoside analogs [e.g., gemcitabine
(Gemzar); Seidman A D., 2001. Oncology (Huntingt). 15: 11-14),
non-steroidal (e.g., anastrozole and letrozole) and steroidal
(exemestane) aromatase inhibitors (Lake D E and Hudis C., 2002;
Cancer Control; 9: 490-8), taxanes and topoisomerase-I inhibitors
(e.g., irinotecan; Van Cutsem, E. 2004; The Oncologist, 9, Suppl 2,
9-15). However, the use of such drugs often fails due to the
development of drug resistance by the cancer cells. Thus, despite
the tremendous progress in understanding tumor biology and early
detection of cancer, cancer mortality rates have not been
significantly reduced.
[0004] The growth of solid tumors depends on nutrients and oxygen
which are supplied by the tumor vasculature. The growth of new
blood vessels into the tumor is controlled by paracrine signals,
many of which are mediated by protein ligands which modulate the
activity of transmembrane tyrosine kinase receptors (RTK). These
include vascular endothelial growth factor (VEGF) and its receptor
families (VEGFR-1, VEGFR-2, neuropilin-1 and neuropilin-2),
Angiopoietins 1-4 (Ang-1, Ang-2) and their respective receptors
(Tie-1 and Tie-2), basic fibroblast growth factor (bFGF), platelet
derived growth factor (PDGF), transforming growth factor .beta.
(TGF-.beta.) and their receptors. Thus, it was conceivable that
inhibition of angiogenesis can inhibit the growth of solid
tumors.
[0005] Indeed, several studies have demonstrated that
anti-angiogenic agents such as Endostatin, AGM-1470, angiostatin,
BB-94, 2-Methoxyestradiol (2-ME) and Taxol in can inhibit tumor
growth in vivo (Boehm et al., 1997; Nature; 390: 404-7; Bergers et
al., 1999; Science; 284: 808-12; Klauber N et al. 1997; 57: 81-6).
However, the mechanisms by which such agents exert their anti-tumor
effect remain unclear (O'Reilly et al., 1997; Oreilly et al.,
1996).
[0006] The interest in FGFs and their receptors as potential drug
targets arose from their wide distribution in cells of different
lineages and their mitogenic and angiogenic activities, two
essential activities for solid tumor growth and metastasis (Zetter,
B. R. 1998; Annu. Rev. Med. 49: 407-424). The oncogenic potential
of FGFs is well documented in both, in-vitro studies and animal
model systems (McKeehan, W. L., et al., 1998; Prog. Nucleic. Acid.
Res. Mol. Biol. 59: 135-176; Szebenyi, G. and Fallon, J. F. 1999;
Int. Rev. Cytol. 185: 45-106; Shaoul, E., et al., 1995; Oncogene
10: 1553-1561; Miki, T., et al., 1991; Science 251: 72-75;
Kitsberg, D. I. and Leder, P. 1996. Oncogene 13: 2507-2515).
Moreover, a variety of human carcinomas including pancreatic,
endometrial and prostate carcinomas, overexpress FGFs (FGF-1, FGF-2
and FGF-7) and their receptors (KGFR and FGFR1), and tumor
aggressiveness is correlated with the level of expression of these
receptors (Giri, D., et al., 1999; Clin. Cancer Res. 5: 1063-1071;
Visco, V., et al., 1999; Int. J. Oncol. 15: 431-435; Siegfried, S.,
et al., 1997; Cancer 79: 1166-1171; Ishiwata, T., et al., 1998; Am.
J. Pathol. 153: 213-222; Kornmann, M., et al., 1998; Pancreas 17:
169-175; Siddiqi, I., et al., 1995; Biochem. Biophys. Res. Commun.
215: 309-315). Altogether, these observations strongly suggest the
involvement of FGFs and their receptors in the malignant process.
Thus, developing tools to target FGFRs, and their signaling
pathways could be very useful for cancer therapy.
[0007] Several mechanisms collectively known as "negative
signaling" have been evolved to attenuate signaling by RTKs
(Christofori, G., 2003). One such mechanism involves ligand-induced
antagonists of RTK signaling. The Sprouty and SPRED (Sprouty
related EVH1-domain-containing) proteins belong to this category,
and are regarded as general inhibitors of RTK signaling. They
suppress the RTK-induced mitogen-activated protein kinase (MAPK)
pathway (reviewed in Christofori, G., 2003; Dikic and Giordano,
2003).
[0008] Sef (for Similar Expression to FGF genes) is a newly
identified antagonist of fibroblast growth factor (FGF) signaling.
Sef encodes a putative type I transmembrane protein that is
conserved across zebrafish, mouse and human but not in
invertebrates (Furthauer, M., et al., 2002; Tsang M., et al., 2002;
Lin, W., et al., 2002). Zebrafish Sef (zfSef) antagonizes FGF
activity during embryogenesis by acting as a feedback-induced
antagonist of the Ras/MAPK mediated FGF-signaling (Furthauer, M.,
et al., 2002; Tsang M., et al., 2002). Subsequent studies showed
that the mouse (Kovalenko D, 2003) homologue of zfSef similarly
inhibit FGF-induced activation of MAPK, and FGF-induced activation
of protein-kinase B (pkB/Akt), a key protein in the
phosphatidylinositol-3 (PI3) kinase pathway. On the other hand, the
mSef was unable to inhibit PDGF-, EGF- or calf serum-induced
phosphorylation of ERK in NIH 3T3 cells (Kovalenko D, 2003). Other
studies showed that the human Sef homologue (which is later
referred to as hSef-a by the present inventor) is capable of
inhibiting FGF- and NGF-induced differentiation of PC12 cells
(Xiong et al., 2003; JBC 278: 50273-50282).
[0009] The expression level of human Sef in normal and malignant
tissues has been controversial. While Yang R B., et al (J. Biol.
Chem. 2003, 278:33232-8) found that Sef is expressed a variety of
breast cancer tissues, Darby S, (Oncogene. 2006, 25: 4122-7) found
that loss of Sef expression is associated with high grade and
metastais of prostate cancer only. Thus, to date, cancer diagnosis
which is based on Sef expression level has not been suggested. In
addition, none of these studies have suggested using Sef expression
for staging of cancer, determining disease course and/or cancer
prognosis and/or for selecting an anti-cancer therapy regimen.
[0010] There is thus, a widely recognized need to develop agents
suitable for diagnosing and treating cancerous solid tumors.
SUMMARY OF THE INVENTION
[0011] While reducing the present invention to practice, the
present inventor has uncovered three new alternatively spliced
isoforms of the human Sef (designated hSefb-d) and demonstrated the
capacity of hSefb to inhibit FGF and PDGF RTK signaling. In
addition, the present inventor has shown that the expression of
hSef is reduced in various solid tumors such as thyroid carcinoma,
breast cancer, ovarian cancer and prostate cancer in a manner which
correlates with an increase in tumor malignancy. Moreover, the
present inventor has demonstrated that overexpression of hSef
results in suppression of colony formation and growth of cancerous
cells. Thus, the present inventor has uncovered that agents capable
of upregulating hSef can be used to inhibit the growth of solid
tumors and thereby treat cancer. In addition, the present inventor
has uncovered that the decrease in hSef expression can be used as a
tool for diagnosing solid tumor, determining disease course and/or
cancer prognosis and/or for selecting an anti-cancer therapy
regimen.
[0012] According to one aspect of the present invention there is
provided a method of inhibiting a growth of a solid tumor in a
subject, the method comprising administering to the subject an
agent capable of upregulating the expression level and/or activity
of at least a functional portion of Sef, the at least a functional
portion of Sef being capable of inhibiting RTK-mediated cell
proliferation, thereby inhibiting the growth of the solid tumor in
the subject.
[0013] According to another aspect of the present invention there
is provided a pharmaceutical composition useful for inhibiting a
growth of a solid tumor in a subject comprising, as an active
ingredient, an agent capable of upregulating the expression level
and/or activity of at least a functional portion of Sef, the at
least a functional portion of Sef being capable of inhibiting
RTK-mediated cell proliferation, and a pharmaceutically acceptable
carrier.
[0014] According to yet another aspect of the present invention
there is provided a method of diagnosing cancer in a subject in
need thereof, the method comprising detecting in a tissue sample of
the subject an expression level of Sef, wherein a decrease in the
expression level of the Sef compared to the expression level of the
Sef in an unaffected tissue is indicative of the cancer, thereby
diagnosing the cancer in the subject in need thereof.
[0015] According to still another aspect of the present invention
there is provided a kit for diagnosing cancer in a subject in need
thereof, the kit comprising a reagent for detecting an expression
level of Sef, wherein a decrease in the expression level of the Sef
compared to the expression level of the Sef in an unaffected tissue
is indicative of the cancer.
[0016] According to further features in preferred embodiments of
the invention described below, the RTK-mediated cell proliferation
is ligand independent.
[0017] According to still further features in the described
preferred embodiments the RTK-mediated cell proliferation is
ligand-induced.
[0018] According to still further features in the described
preferred embodiments the at least a functional portion of Sef is a
polypeptide as set forth by SEQ ID NO:6.
[0019] According to still further features in the described
preferred embodiments the at least a functional portion of Sef is a
polypeptide as set forth by amino acid coordinates 1-10, 267-707
and/or 288-707 of SEQ ID NO:6.
[0020] According to still further features in the described
preferred embodiments upregulating is effected by at least one
approach selected from the group consisting of:
[0021] (a) expressing in cells of the subject an exogenous
polynucleotide encoding at least a functional portion of Sef;
[0022] (b) increasing expression of endogenous Sef in cells of the
subject;
[0023] (c) increasing endogenous Sef activity in cells of the
subject; and
[0024] (d) introducing an exogenous peptide and/or exogenous
polypeptide including at least a functional portion of Sef to the
subject.
[0025] According to still further features in the described
preferred embodiments the exogenous polynucleotide is a nucleic
acid construct comprising a polynucleotide at least 90% identical
to the polynucleotide sequence set forth in SEQ ID NO:4.
[0026] According to still further features in the described
preferred embodiments the exogenous polynucleotide is a nucleic
acid construct comprising a polynucleotide selected from the group
consisting of SEQ ID NOs:4, 8, and 9.
[0027] According to still further features in the described
preferred embodiments the nucleic acid construct further comprises
a promoter capable of directing an expression of the polynucleotide
in the cells of the subject.
[0028] According to still further features in the described
preferred embodiments the promoter is selected from the group
consisting of Cytomegalovirus (CMV) promoter, simian virus (SV)-40
early promoter, SV-40 late promoter, metallothionein promoter,
murine mammary tumor virus promoter, Rous sarcoma virus (RSV)
promoter, and
[0029] According to still further features in the described
preferred embodiments the Sef is a polypeptide at least 90%
homologous (identical+similar) to a polypeptide set forth by SEQ ID
NO:6 as determined using the BlastP software where gap open penalty
equals 11, gap extension penalty equals 1 and matrix is blosum
62.
[0030] According to still further features in the described
preferred embodiments the Sef is a polypeptide set forth by SEQ ID
NO:6.
[0031] According to still further features in the described
preferred embodiments the solid tumor is selected from the group
consisting of ovarian carcinoma, pancreatic cancer, breast cancer,
endometrial carcinoma, brain tumor, adrenal carcinoma, pituitary
cancer, thyroid carcinoma, tonsillar carcinoma, spleen cancer,
adenoids cancer, kidney cancer, liver cancer, testis cancer,
bladder cancer, colon cancer, prostate cancer, bile duct, lung
cancer, and stomach cancer.
[0032] According to still further features in the described
preferred embodiments the ligand is selected from the group
consisting of FGF, PDGF, VEGF, NGF, insulin, and EGF.
[0033] According to still further features in the described
preferred embodiments the RTK-mediated cell proliferation is
effected by inhibition of activated Erk1/2 (P-Erk1/2) within the
cells.
[0034] According to still further features in the described
preferred embodiments the cancer is a solid tumor.
[0035] According to still further features in the described
preferred embodiments the solid tumor is selected from the group
consisting of breast cancer, ovarian cancer, thyroid carcinoma and
prostate cancer.
[0036] According to still further features in the described
preferred embodiments the Sef is a nucleic acid sequence of
Sef.
[0037] According to still further features in the described
preferred embodiments the Sef is an amino acid sequence of Sef.
[0038] According to still further features in the described
preferred embodiments detecting is effected by an RNA detection
method.
[0039] According to still further features in the described
preferred embodiments detecting is effected by a protein detection
method
[0040] According to still further features in the described
preferred embodiments the RNA detection method is selected from the
group consisting of RNA in situ hybridization, RT-PCR, in situ
RT-PCR and Northern blot analysis.
[0041] According to still further features in the described
preferred embodiments the protein detection method is selected from
the group consisting of ELISA, Western blot, immunofluorescence and
immunohistochemical analysis.
[0042] According to still further features in the described
preferred embodiments the solid tumor is a primary solid tumor.
[0043] According to still further features in the described
preferred embodiments the Sef is Sef-a and whereas the solid tumor
is breast cancer or ovarian cancer.
[0044] According to still further features in the described
preferred embodiments the Sef is Sef-b and whereas the solid tumor
is thyroid carcinoma.
[0045] According to still further features in the described
preferred embodiments the method further comprising determining a
malignancy of the solid tumor.
[0046] According to still further features in the described
preferred embodiments the reagent is utilized for an RNA detection
method.
[0047] According to still further features in the described
preferred embodiments the reagent is utilized in a protein
detection method.
[0048] According to still further features in the described
preferred embodiments the reagent is an isolated nucleic acid
sequence complementary to the Sef nucleic acid sequence.
[0049] According to still further features in the described
preferred embodiments the reagent is an antibody or antibody
fragment which comprises an antigen recognition region capable of
specifically binding the Sef amino acid sequence.
[0050] The present invention successfully addresses the
shortcomings of the presently known configurations by providing
agents and pharmaceutical compositions suitable for inhibiting the
growth of solid tumors and methods and kits for diagnosing cancer,
and/or for selecting an anti-cancer therapy regimen.
[0051] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, suitable methods and materials are described below. In
case of conflict, the patent specification, including definitions,
will control. In addition, the materials, methods, and examples are
illustrative only and not intended to be limiting.
BRIEF DESCRIPTION OF THE DRAWINGS
[0052] The invention is herein described, by way of example only,
with reference to the accompanying drawings. With specific
reference now to the drawings in detail, it is stressed that the
particulars shown are by way of example and for purposes of
illustrative discussion of the preferred embodiments of the present
invention only, and are presented in the cause of providing what is
believed to be the most useful and readily understood description
of the principles and conceptual aspects of the invention. In this
regard, no attempt is made to show structural details of the
invention in more detail than is necessary for a fundamental
understanding of the invention, the description taken with the
drawings making apparent to those skilled in the art how the
several forms of the invention may be embodied in practice.
[0053] In the drawings:
[0054] FIG. 1 is a schematic illustration depicting the structural
homology between the human Sef-a and Sef-b isoforms. Shown are
residues unique in each Sef isoform (bold letters), the signal for
secretion (asterisk), potential N-linked glycosylation sites
(arrows), transmembrane domain (black box), putative tyrosine
phosphorylation site (Y), immunoglobulin like domain and the
IL-17R-like domain (light and dark gray boxes). Note that while the
human Sef-a contains a signal for secretion (the sequence appears
left to the arrow), the hSef-b isoform lacks such a signal.
[0055] FIGS. 2a-b are autoradiographs depicting the identification
of hSef protein products. FIG. 2a--Western blot analysis. HEK 293
cells were transiently transfected with either a control empty
vector (lane 1) or Myc-tagged hSef-b or hSef-a vectors (lanes 2 and
3, respectively). Equal amounts of protein were subjected to
SDS-PAGE followed by a-myc immunoblotting. FIG. 2b--in-vitro
translation of hSef-b. In vitro transcription-translation was
performed in the presence of [.sup.35S] -methionine and either an
expression vector including the hSef-b cDNA (lane 1) or an empty
vector (lane 2). The translation products were analyzed by
SDS-PAGE, and visualized by phospho-imaging.
[0056] FIGS. 3a-d are immunofluorescence staining depicting the
cellular localization of the hSef isoforms. HEK 293 cells were
transfected with the myc-tagged hSef-a (FIGS. 3a and b) or the
myc-tagged hSef-b (FIG. 3c and d) expression vectors, and 48 hours
post-transfection the cells were subjected to immunostaining using
.alpha.-myc (red; Figures a and c) or .alpha.-hSef (green; FIG. 3b
and d) antibodies. Nuclei were counterstained with bisbenzimide
(blue).
[0057] FIGS. 4a-d are agarose gel images depicting the expression
pattern of human Sef isoforms as determined by RT-PCR analyses.
Total RNA from the indicated human tissues and human primary cells
was subjected to RT-PCR using primers specific to the common hSef
transcript (SEQ ID NOs:11 and 18, FIG. 4a), to the hSef-a (SEQ ID
NOs:17 and 16, FIG. 4b), hSef-b (SEQ ID NOs:2 and 17, FIG. 4c), or
GAPDH (SEQ ID NOs:12 and 13). Adrenal m=adrenal medulla; adrenal
c=adrenal cortex; A.E. cells=primary aortic endothelial cells; F.
Brain=fetal brain; A. Brain=adult brain; F. Kidney=fetal kidney;
NC=negative control; PC=positive control. Templates for positive
controls are plasmids containing hSef-a (FIGS. 4a-b); hSef-b (FIG.
4c) or GAPDH (FIG. 4d).
[0058] FIG. 5 is an autoradiograph depicting induced expression of
hSef-b in the Tet-off NIH/3T3 cells. Cells were grown in 10% serum
in the presence (lanes 1 and 3) or absence (lanes 2 or 4) of
tetracycline. Following 24 hours, the cells were lysed and hSef-b
expression was analyzed by immunoblotting with hSef specific
antibodies. Lanes 1 and 2=Control cultures of parental cells
transfected with an empty pTet-Splice vector; lanes 3 and 4=Cells
transfected with the pTet-Splice-hSef-b vector.
[0059] FIGS. 6a-c are photomicrographs illustrating the effect of
hSef-b on apoptosis. NIH/3T3/hSef-b cells were grown for 48 hours
in the presence (FIGS. 6a) or absence (FIGS. 6b and 6c) of
tetracycline, and in the absence of tetracycline and serum (FIG.
6c). Cells were washed, fixed and apoptosis was then evaluated by
TUNEL staining. Note the presence of apoptotic cells in the absence
of tetracycline and serum (FIG. 6c).
[0060] FIGS. 7a-b are graphs illustrating the inhibition of the
mitogenic activity of FGF2 by human Sef-b. Confluent cultures of
control (FIG. 7a) or hSef-b expressing (FIG. 7b) cells were serum
starved (in the presence of 0.2% serum) for 24 hours in the
presence or absence of tetracycline. FGF2 was added at the
above-indicated concentrations and [.sup.3H]-thymidine
incorporation assay was performed as previously described (24,
26).
[0061] FIG. 8 is a Western Blot analysis illustrating the effect of
hSef-b on cyclin D1 levels. Human Sef-b inducible NIH/3T3 cells
were serum starved for 24 hours in the presence (lanes 1-5) or
absence (lanes 6-10) of tetracycline, following which the cells
were stimulated with FGF2 (20 ng/ml) for 0 (lanes 1 and 6), 5
(lanes 2 and 7), 8 (lanes 3 and 8), 12 (lanes 4 and 9), or 20
(lanes 5 and 10) hours. The levels of cyclin D1 were evaluated in
total cell lysates over 20 hours of stimulation. Cyclin D1 and CDK
proteins were analyzed by immunoblotting with anti-D1 monoclonal
antibody and rabbit anti-CDK4, respectively. Note the presence of
the Cyclin D1 protein in cells grown with tetracycline and the
absence of such protein following tetracycline removal and
activation of hSef-b expression.
[0062] FIGS. 9a-b are Western Blot analyses illustrating the effect
of hSef-b on FGF2-induced signaling pathways. FIG. 9a--NIH 3T3
hSef-b expressing cells; FIG. 9b--NIH 3T3 cells transfected with an
empty vector (control cultures). Equal amounts of total cells
lysates were analyzed by immunoblotting. The membranes were
successively incubated with the indicated antibodies. Lanes 1-4:
cells were grown in the presence of tetracycline; lanes 5-8: cells
were grown in the absence of tetracycline. Note that while in cells
transfected with the control empty vector Erk1/2 activation was not
influenced by tetracycline removal (FIG. 9b), in hSef-b-expressing
cells tetracycline removal resulted in a decrease in the level of
P-Erk1/2, but not the level of total Erk1/2. Each experiment was
repeated at least twice and using two independent clones of hSef-b
inducible cells. P-Erk 1/2, P-Akt, P-p38 and P-MEK1/2 are
antibodies directed against the phosphorylated (P) form of each of
the kinases.
[0063] FIGS. 10a-b are autoradiographs illustrating
co-immunoprecipitation analyses of Sef isoforms and FGFR1. HEK 293
cells were transfected with the indicated constructs and
immunoblotting with .alpha.-FGFR1 (H76) or .alpha.-hSef antibodies
was performed on whole cell lysates (WCL; FIG. 10b) or on cell
lysates following .alpha.-myc immunoprecipitation (IP; FIG. 10a).
Lane 1--transfection with the FGFR1 construct; lane 2--transfection
with hSef-a construct containing the c-myc epitop at the C-terminus
(hSef-a::myc); lane 3--co-transfection with the FGFR1 and the
hSef-a::myc constructs; lane 4=transfection with the hSef-b
construct containing the c-myc epitop at the C-terminus
(hSef-b::myc); lane 5--co-transfection with the FGFR1 and the
hSef-b::myc constructs.
[0064] FIGS. 11a-b are bar graphs depicting mitogenic assays in
control (FIG. 11a) or hSef-b expressing (FIG. 11b) cells. Confluent
cultures were subjected to mitogenic assays as describe in FIGS.
7a-b and the fold increase (FI) in biological activity was
calculated by dividing CPM values obtained in the presence of the
indicated stimulators with those obtained in the presence of 0.2%
serum alone. Percent [.sup.3H]-thymidine incorporation is relative
to FI obtained in cultures stimulated with 10% serum in the
presence of tetracycline that was set as 100%. The concentrations
of FGFs, insulin, EGF and serum are those which gave rise to a
maximal biological response. F=FGF; INS=insulin.
[0065] FIG. 12 is a Western Blot analysis illustrating the effect
of hSef-b-mediated PDGF inhibition of ERK1/2 MAPK level. Human
Sef-b inducible NIH/3T3 cells were serum starved for 24 hours in
the presence (lanes 1-3) or absence (lanes 4-6) of tetracycline,
following which the cells were stimulated with 20 ng/ml PDGF for
the indicated time periods. Equal amounts of total cells lysates
were analyzed by immunoblotting using anti-P-Erk 1/2 and anti-ERK
antibodies. These experiments were repeated at least 3 times and
using two independent hSef-b expressing clones.
[0066] FIGS. 13a-b depict the nucleic acid (FIG. 13a) and amino
acid (FIG. 13b) sequences of hSef-c as determined using the RACE
products. Nucleic acids and amino acids from the unique hSef-c
domain are labelled in red. The potential initiation Methionine
codons are labelled in green. *=termination codon.
[0067] FIGS. 14a-b depict the nucleic acid (FIG. 14a) and amino
acid (FIG. 14b) sequences of hSef-d as determined using the RACE
products. Nucleic acids and amino acids from the unique hSef-d
domain are labelled in red. The potential initiation Methionine
codon is labelled in green.
[0068] FIGS. 15a-i depict the expression of hSef in normal human
breast and breast cancer. FIG. 15a--RT-PCR analysis of hSef A and B
isoforms and GAPDH standard using total RNA from normal human
breast tissue. n.c.: negative control, template minus. p.c.:
positive control using hSefA expression vector as template for
amplification. FIGS. 15b-c--RNA in-situ hybridization visualizing
very strong hSef expression in normal ductal epithelium. FIG.
15c--higher magnification of intra-lobular ducts. Ep and F denote
epithelial cells and stromal fibroblasts, respectively. FIG.
15d--Breast hyperplasia (red arrow) and coexisting low grade ductal
carcinoma in situ (black arrow) exhibiting nearly normal hSef
levels; FIG. 15e--heterogeneous hSef expression in low-grade well
differentiated invasive carcinoma; strong expression (black arrow,
and inset) in intraductal cancer cells, and very low expression
(red arrow) in areas of lower differentiation. FIGS.
15f-i--Invasive breast carcinomas harboring low expression or loss
of hSef. Low hSef expression in infiltrating ductal carcinoma grade
I (FIG. 15f), and lack of hSef expression in two cases of
infiltrating ductal carcinoma grade II (FIGS. 15g-h), and a
scirrhous carcinoma grade II (FIG. 15i). Arrow in FIG. 15g
indicates hSef-positive normal duct surrounded by negative cancer
tissue. Bars: 100 .mu.m. Magnification in FIGS. 15b, c-d, and f-i
is X160, X45, X25, respectively.
[0069] FIGS. 16a-f are in situ hybridization analyses depicting
down-regulation of hSef in ovarian carcinoma. Strong hSef
expression in normal ovarian surface epithelium (OSE, FIG. 16a) and
epithelial lining of the fallopian tube (FT, FIG. 16b). Examples of
hSef expression levels in ovarian carcinomas of varying grades
including serous papillary cystic adenocarcinoma grade I expressing
strong hSef levels (FIG. 16c); grade II with moderate (FIG. 16d)
and grade II with low expression level (FIG. 16e); grade III tumor
negative for hSef expression. Bars: 25 .mu.m (FIG. 16a) and 100
.mu.m (FIGS. 16b-f).
[0070] FIGS. 17a-f are in situ hybridization analyses depicting
expression of hSef in normal thyroid gland and thyroid carcinoma.
High hSef expression in follicular cells of normal thyroid (FIGS.
17a, b). Strong or moderate hSef levels in two cases of low-grade
papillary carcinoma (FIGS. 17c, d). In FIG. 17d, note negative
staining (arrow on the bottom right) and moderate hSef signal in
areas of higher differentiation (arrow on top left, FIG. 17d).
Negative hSef staining in papillary (FIG. 17e) and follicular (FIG.
17f) carcinoma. Bars: 25 .mu.m (FIGS. 17a-b); 100 .mu.m (FIGS.
17c-f).
[0071] FIGS. 18a-f are in situ hybridization analyses depicting
expression of hSef mRNA in normal prostate and prostate tumors.
FIG. 18a--Strong hSef expression in glandular epithelium (black
arrow) and weaker hSef signal of stromal fibroblasts in normal
prostate. FIG. 18b--Down-regulation of hSef in BPH; FIG.
18c--heterogenous hSef expression in low-grade (GG6) prostate
adenocarcinoma. Arrowhead points to a normal gland, and arrows to
malignant glands with moderate hSef levels (black arrow) or
negative hSef staining (red arrow). FIGS. 18d-e--two intermediate
grade prostate adenocarcinoma (GG7) with low or negative hSef
staining. FIG. 18f--High grade prostate adenocarcinoma negative for
hSef expression. Counterstain with Hematoxylin. Bars: 100
.mu.m.
[0072] FIGS. 19a-b depict that silencing hSef expression enhances
cell proliferation. For hSef RNA silencing, HeLa cells were
transfected with the pSUPER vector bearing hSef sh-RNA (Sef-sh) or
pSUPER containing control sh-RNA (Ct-sh). Mass cultures of
resistant cells were prepared as described in Materials and
Methods. FIG. 19a--RT-PCR analysis of total RNA extracted from
transfected cells to determine the extent of hSef silencing. Top
panel: hSef, bottom panel: GAPDH. Primers common to hSef isoforms
were utilized for amplification (top panel).-RT: first strand was
synthesized in the absence of reverse transcriptase; PC: positive
control for amplification using hSef expression vector as template.
FIG. 19b--HeLa cells stably expressing hSef shRNA (shaded bars) or
control shRNA (solid bars) were seeded at a density of 25,000
cell/35 mm plate, and 24 hours later cells were washed and grown
under serum free conditions in the absence or presence of the
indicated growth factors. Growth factors were added every other
day, and live cells were counted 5 days post seeding. The error
bars indicate standard deviation of 3 independent experiments.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0073] The present invention is a method of inhibiting solid tumor
growth using an agent capable of upregulating the expression level
and/or activity of hSef-b in FGF and/or PDGF-induced proliferating
cancerous cells, and tumors that overexpress their cognate
receptors. Specifically, the present invention can be used to treat
cancerous tumors such as ovarian carcinoma, pancreatic cancer,
breast cancer, endometrial carcinoma and brain tumors. In addition,
the present invention is of methods and kits for diagnosing cancer
and selecting an anti-cancer treatment regimen by detecting a
decrease in the expression level of Sef in a tissue sample.
[0074] The principles and operation of the method of inhibiting
solid tumor growth and diagnosing cancer according to the present
invention may be better understood with reference to the drawings
and accompanying descriptions.
[0075] Before explaining at least one embodiment of the invention
in detail, it is to be understood that the invention is not limited
in its application to the details set forth in the following
description or exemplified by the Examples. The invention is
capable of other embodiments or of being practiced or carried out
in various ways. Also, it is to be understood that the phraseology
and terminology employed herein is for the purpose of description
and should not be regarded as limiting.
[0076] Solid tumors account for the majority of human tumors and
among them, carcinomas of an epithelial origin, account for over
80%. Conventional cancer therapy is based on chemotherapy drugs
(e.g., thymidylate synthase inhibitors, nucleoside analogs,
aromatase inhibitors, taxanes and topoisomerase-I inhibitors) which
often fail due to the development of drug resistance by the
cancerous cells.
[0077] Since the growth of solid tumors depends on nutrients and
oxygen which are supplied by the tumor vasculature, new approaches
of cancer therapy are focused on the inhibition of angiogenesis via
the inhibition of receptor tyrosine kinases and their ligands.
Thus, various anti-angiogenic agents have been designed and tested
in animal models (Boehm et al., 1997; Nature; 390: 404-7; Bergers
et al., 1999; Science; 284: 808-12; Klauber N et al. 1997; 57:
81-6). However, the mechanisms by which such agents exert their
anti-tumor effect remain unclear (O'Reilly et al., 1997; Oreilly et
al., 1996).
[0078] Recently, new ligand-induced antagonists of RTK signaling
have been discovered. These include the Sprouty and SPRED (Sprouty
related EVH1-domain-containing) proteins which suppress the
RTK-induced mitogen-activated protein kinase (MAPK) pathway
(reviewed in Christofori, G., 2003; Dikic and Giordano, 2003).
[0079] Sef (for Similar Expression to FGF genes) is a newly
identified antagonist of fibroblast growth factor (FGF) signaling
which antagonizes FGF activity during embryogenesis by acting as a
feedback-induced antagonist of the Ras/MAPK mediated FGF-signaling
(Furthauer, M., et al., 2002; Tsang M., et al., 2002). Sef encodes
a putative type I transmembrane protein that is conserved across
zebrafish, mouse and human (Yang R B, et al., 2003 and data not
shown) but not in invertebrates (Furthauer, M., et al., 2002; Tsang
M., et al., 2002; Lin, W., et al., 2002). Subsequent studies showed
that the mouse (Kovalenko D, 2003) homologue of zfSef similarly
inhibits FGF-induced activation of MAPK, and FGF-induced activation
of protein-kinase B (pkB/Akt), a key protein in the
phosphatidylinositol-3 (PI3) kinase pathway. On the other hand, the
mSef was unable to inhibit PDGF-, EGF- or calf serum-induced
phosphorylation of ERK in NIH 3T3 cells (Kovalenko D, 2003). Other
studies showed that the human Sef homologue (which is later
referred to as hSef-a by the present inventor), is capable of
inhibiting FGF- and NGF-induced differentiation of PC12 cells
(Xiong et al., 2003; JBC 278: 50273-50282).
[0080] FGFs comprise a family of 22 structurally related
polypeptide mitogens that control cell proliferation,
differentiation, survival and migration, and play a key role in
embryonic patterning (14-16). They signal via binding and
activation of a family of cell surface tyrosine kinase receptors
designated FGFR1-FGFR4 (17-20). Activated receptors trigger several
signal transduction cascades including the Ras/MAPK and the
PI3-kinase pathway (15, 21). Depending on the cell type, FGF can
also activate other MAPK pathways, such that leading to the
activation of p38-MAPK (22, 23).
[0081] PDGF acts as a potent mitogen of mesenchymal cell
proliferation via the two related receptor tyrosine kinases, alpha
and beta PDGF receptors and its expression was demonstrated in
various solid tumors, such as glioblastomas and prostate carcinomas
(Reviewed in George D. 2003; Adv Exp Med Biol. 532:141-51).
[0082] The expression of human Sef in normal and malignant tissues
has been controversial. While Yang R B., et al (J. Biol. Chem.
2003, 278:33232-8) found that Sef is expressed a variety of breast
cancer tissues, Darby S, (Oncogene. 2006, 25: 4122-7) found that
loss of Sef expression is associated with high grade and metastais
of prostate cancer only. Thus, to date, cancer diagnosis based on
the expression level of Sef has not been suggested. In addition,
none of these studies have suggested using Sef expression for
staging of cancer, determining disease course and/or cancer
prognosis and/or for selecting an anti-cancer therapy regimen.
[0083] While reducing the present invention to practice, the
present inventor has uncovered three new alternatively spliced
isoforms of the human Sef (designated hSefb-d) and demonstrated
that hSef-b is uniquely capable of inhibiting FGF and PDGF RTK
signaling, inhibiting the growth of cells expressing FGF and PDGF
cognate receptors and reducing solid tumor growth. In addition, the
present inventor has shown that the expression of hSef is reduced
in various solid tumors such as thyroid carcinoma, breast cancer,
ovarian cancer and prostate cancer in a manner which correlates
with an increase in tumor malignancy. Moreover, the present
inventor has demonstrated that overexpression of hSef results in
suppression of colony formation and growth of cancerous cells.
Thus, the present inventor has uncovered that agents capable of
upregulating hSef can be used to inhibit the growth of solid tumors
and thereby treat cancer. In addition, the present inventor has
uncovered that the decrease in hSef expression can be used as a
tool for diagnosing solid tumor, including staging of cancer,
determining disease course and/or cancer prognosis and/or for
selecting an anti-cancer therapy regimen.
[0084] As is shown in FIGS. 1-4 and Examples 1 and 2 of the
Examples section which follows, while the hSef-a protein is a
heavily glycosylated membrane protein, the hSef-b protein is a
cytosolic protein, lacking post-translational glycosylations.
Furthermore, the cytosolic isoform of the human Sef protein
(hSef-b), but not the transmembrane isoform (hSef-a, See Lin W., et
al., 2002) is capable of inhibiting the growth of NIH/3T3 cells via
the inhibition of FGF and PDGF signaling pathway (FIGS. 1-2 and
4-12, Table 1 and Examples 1, 3, 4, and 5 of the Examples section
which follows). In addition, as is shown in FIGS. 2a-b and Example
1 of the Examples section which follows, hSef-b is translated from
a Leucine initiation codon instead of a Methionine codon. Such a
usage of an alternative translation initiation codon is probably
the reason for the relatively low levels of hSef-b obtained
following transfection (data not shown). Notwithstanding, hSef-b
was found to be more potent in inhibiting RTK-mediated cell
proliferation than hSef-a (data not shown). Altogether, these
results demonstrate that the unique N-terminal sequence of hSef-b
(amino acids 1-10 in SEQ ID NO:6) and/or the lack of secretion
signal and/or the intracellular location of hSef-b confer upon this
protein (hSef-b) unique properties as a potent inhibitor of
RTK-mediated cell proliferation with a wide repertoire of
substrates and/or interacting proteins. As is further shown in
Table 2 and is described in Example 7 of the Examples section which
follows, over-expression of either hSef-a, hSef-b or hSef-c in
breast cancer cells resulted colony suppression and growth
inhibition. Moreover, as is shown in FIGS. 15-20 and Tables 3-6 and
is described in Example 8 of the Examples section which follows, in
situ hybridization analyses demonstrated that hSef is downregulated
in various solid tumors such as breast cancer, ovarian cancer,
prostate cancer and thyroid carcinoma, suggesting that
downregulation of hSef is a common mechanism in cancer. Thus, out
of a total of 155 primary carcinoma cases that were screened hSef
expression was completely lost in 100/155 cases and reduced in the
remaining 55 cases.
[0085] Thus, according to one aspect of the present invention there
is provided a method of inhibiting a growth of a solid tumor in a
subject.
[0086] As used herein, the phrase "inhibiting a growth" refers to
arresting the development, causing the reduction, remission, or
regression of a solid tumor, eradicating tumor cells and/or
preventing tumor metastasis. Those of skill in the art will be
aware of various methodologies and assays which can be used to
assess the development of a solid tumor (e.g., biopsy or fine
needle aspiration followed by histopathological examination,
ultrasound scan, C.T. scan, X-ray, NMR and the like), and
similarly, various methodologies and assays which can be used to
assess the reduction, remission or regression of the solid
tumor.
[0087] The phrase "solid tumor" as used herein, refers to an
abnormal mass of tissue resulting from excessive cell division.
Solid tumors can be benign or cancerous (i.e., with unregulated
proliferation). Preferably, the phrase "solid tumor" as used herein
relates to an unregulated cancerous tumor including, but not
limited to, ovarian carcinoma, pancreatic cancer, breast cancer,
endometrial carcinoma, brain tumor, adrenal carcinoma, pituitary
cancer, thyroid carcinoma, tonsillar carcinoma, spleen cancer,
adenoids cancer, kidney cancer, liver cancer, testis cancer,
bladder cancer, colon cancer, prostate cancer, bile duct, lung
cancer, stomach cancer, and the like.
[0088] The method is effected by administering to the subject an
agent capable of upregulating the expression level and/or activity
of at least a functional portion of Sef, such a functional portion
of Sef being capable of inhibiting RTK-mediated cell proliferation,
thereby inhibiting the growth of the solid tumor in the
subject.
[0089] As used herein, the term "subject" refers to a mammal,
preferably a human being (male or female) at any age which is
diagnosed with a cancerous solid tumor as described hereinabove or
is predisposed to developing such a tumor.
[0090] According to preferred embodiments of the present invention
the functional portion of Sef encompasses a Sef protein derived
sequence (i.e., of any of the hSef isoforms and homologues
described herein, preferably hSef-b) which is functional as an RTK
receptor antagonist and thus is capable of inhibiting RTK-mediated
cell proliferation via the inhibition of activated ERK1/2.
[0091] It will be appreciated that since hSef-b (SEQ ID NO:6) lacks
the secretion signal and is found entirely in the cytosol, its
entire coding sequence (i.e., amino acid 1-707 in SEQ ID NO:6) can
potentially contribute to its functional activity (i.e., inhibiting
RTK mediated cell proliferation).
[0092] Thus, according to preferred embodiments of the present
invention the functional portion of Sef is encompassed by the
sequence set forth by amino acids 1-707 of SEQ ID NO:6.
[0093] Since hSef-a and hSef-b share a large common domain (i.e.,
amino acids 11-707 of SEQ ID NO:6) of which a large portion is
cytosolic [i.e., amino acids 320-739 in SEQ ID NO:5 (hSef-a) which
are identical to amino acids 288-707 in SEQ ID NO:6 (hSef-b)], the
functional portion of Sef is preferably encompassed by amino acids
288-707 of SEQ ID NO:6.
[0094] Additionally or alternatively, based on targeted deletions
made using hSef-a DNA constructs (Xiong S., et al., 2003, JBC 278:
50273-50282; Torii S., et al., 2004, Developmental Cell 7:33-44)
which demonstrated the presence of domains required for hSef-a
activity, it is conceivable that the equivalent sequence in hSef-b
would contribute to the functional activity of hSef-b, i.e.,
inhibiting RTK-mediated cell proliferation. Thus, the functional
portion of Sef is preferably encompassed by amino acids 267-707 of
SEQ ID NO:6.
[0095] Yet additionally or alternatively, since as is mentioned
above hSef-b is a more potent inhibitor of RTK-mediated cell
proliferation than hSef-a, it is conceivable that the unique
sequence of hSef-b (i.e., amino acids 1-10 in SEQ ID NO:6) is
likely to contribute to the functional activity of Sef. Thus,
according to preferred embodiments of the present invention the
functional portion of Sef includes at least amino acids 1-10 of SEQ
ID NO:6, more preferably, at least amino acids 1-10 and 267-707 of
SEQ ID NO:6, more preferably, at least amino acids 1-10 and 288-707
of SEQ ID NO:6.
[0096] It will be appreciated that the method of the present
invention can also utilize Sef homologues (identified from other
species or other hSef isoforms) which exhibit the above described
functional activity.
[0097] Preferably, the polypeptide used by the present invention is
at least 85%, at least 86%, at least 87%, at least 88%, at least
89%, at least 90%, at least 91%, at least 92%, at least 93%, at
least 94%, at least 95%, at least 96%, at least 97%, at least 98%,
most preferably, at least 99% homologous (similar +identical) to
the polypeptide sequence set forth in SEQ ID NO:6 or to a portion
thereof, as determined using the BlastP software available from the
NCBI (http://www.ncbi.nlm.nih.gov) where gap open penalty equals
11, gap extension penalty equals 1 and matrix is blosum 62.
[0098] As used herein, the phrase "RTK-mediated cell proliferation"
refers to RTK activation, signaling and/or over-expression which
can be either ligand-induced or ligand independent. Non-limiting
examples of RTK ligands include FGF, PDGF, NGF, VEGF, insulin,
PLGF, c-kit, met and EGF. Ligand independent RTK-mediated cell
proliferation is often found in cancerous tumors such as
neuroblastoma [e.g., TrkA (Gryz E A and Meakin S O, 2003; Oncogene.
22: 8774-85)], gliomas (Kapoor G S and O'Rourke D M, 2003, Cancer
Biol. Ther. 2: 330-42), lung cancer [e.g., c-Met (Ma P C, et al.,
2003; Cancer Res. 63: 6272-81)], breast and prostate cancers [e.g.,
HER2 (Witton C J et al., 2003, J Pathol. 200: 290-7)].
[0099] As is mentioned hereinabove, the present invention
preferably targets the RTKs ligands FGF and PDGF. It will be
appreciated that activity of other RTK ligands which are capable of
inducing cell proliferation via the activation of ERK1/2, can also
be inhibited by the various hSef isoforms of the present
invention.
[0100] It is also highly likely that unique sequences present in
splice variants hSef-c (i.e., amino acids 8-49, 9-49 or 28-49 of
SEQ ID NO:15) and hSef-d (i.e., amino acids 37-50 of SEQ ID NO:14)
are involved in specific RTK-mediated cell proliferation and/or
signaling and as such, the present invention also envisages using
these sequences in the method of the present invention.
[0101] As is mentioned hereinabove, the present method is effected
by upregulating the expression level and/or activity of at least a
functional portion of Sef.
[0102] The term "upregulating" relates to increasing the expression
and/or activity of Sef.
[0103] Upregulation of Sef can be effected at the genomic level
(i.e., activation of transcription via promoters, enhancers,
regulatory elements), at the transcript level (i.e., correct
splicing, polyadenylation, activation of translation) or at the
protein level (i.e., post-translational modifications, interaction
with substrates and the like). For example, upregulation can be
effected using hormones or their agonists which upregulate Sef
transcription or stabilize Sef RNA transcripts as is further
described hereinbelow.
[0104] Following is a list of agents capable of upregulating the
expression level and/or activity of Sef.
[0105] An agent capable of upregulating expression level of a Sef
may be an exogenous polynucleotide sequence designed and
constructed to express at least a functional portion of the Sef
protein. Accordingly, the exogenous polynucleotide sequence may be
a DNA or RNA sequence encoding a Sef molecule, capable of
inhibiting RTK ligand-induced cell proliferation.
[0106] The entire coding region of Sef has been cloned from
Zebrafish, mouse, human and chicken and partial cDNA clones are
also available from bovine. Thus, coding sequences information for
Sef is available from several databases including the GenBank
database available through http://www.ncbi.nlm.nih.gov/.
[0107] To express exogenous Sef in mammalian cells, a
polynucleotide sequence encoding Sef (SEQ ID NO:6) or a functional
portion of Sef (amino acids 1-707 of SEQ ID NO:6 or a portion
thereof) is preferably ligated into a nucleic acid construct
suitable for mammalian cell expression. Such a nucleic acid
construct includes a promoter sequence for directing transcription
of the polynucleotide sequence in the cell in a constitutive or
inducible manner.
[0108] It will be appreciated that the nucleic acid construct of
the present invention can also utilize Sef homologues encoding
polypeptides which exhibit the desired activity (i.e., inhibiting
RTK-mediated cell proliferation). Such homologues can be, for
example, at least 85%,at least 86%, at least 87%, at least 88%, at
least 89%, at least 90%, at least 91%, at least 92%, at least 93%,
at least 94%, at least 95%, at least 96%, at least 97%, at least
98%, at least 99% or 100% identical to SEQ ID NO:4 or a portion
thereof, as determined using the BestFit software of the Wisconsin
sequence analysis package, utilizing the Smith and Waterman
algorithm, where gap weight equals 50, length weight equals 3,
average match equals 10 and average mismatch equals -9.
[0109] Constitutive promoters suitable for use with the present
invention are promoter sequences which are active under most
environmental conditions and most types of cells such as the
cytomegalovirus (CMV) and Rous sarcoma virus (RSV). Inducible
promoters suitable for use with the present invention include for
example the tet off system (Shockett, P., Difilippantonio, M.,
Hellman, N. & Schatz, D. G. (1995) Proc. Natl. Acad. Sci.
U.S.A. 92: 6522-6526).
[0110] The nucleic acid construct (also referred to herein as an
"expression vector") of the present invention includes additional
sequences which render this vector suitable for replication and
integration in prokaryotes, eukaryotes, or preferably both (e.g.,
shuttle vectors). In addition, a typical cloning vectors may also
contain a transcription and translation initiation sequence,
transcription and translation terminator and a polyadenylation
signal.
[0111] Eukaryotic promoters typically contain two types of
recognition sequences, the TATA box and upstream promoter elements.
The TATA box, located 25-30 base pairs upstream of the
transcription initiation site, is thought to be involved in
directing RNA polymerase to begin RNA synthesis. The other upstream
promoter elements determine the rate at which transcription is
initiated.
[0112] Enhancer elements can stimulate transcription up to 1,000
fold from linked homologous or heterologous promoters. Enhancers
are active when placed downstream or upstream from the
transcription initiation site. Many enhancer elements derived from
viruses have a broad host range and are active in a variety of
tissues. For example, the SV40 early gene enhancer is suitable for
many cell types. Other enhancer/promoter combinations that are
suitable for the present invention include those derived from
polyoma virus, human or murine cytomegalovirus (CMV), the long term
repeat from various retroviruses such as murine leukemia virus,
murine or Rous sarcoma virus and HIV. See, Enhancers and Eukaryotic
Expression, Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
1983, which is incorporated herein by reference.
[0113] In the construction of the expression vector, the promoter
is preferably positioned approximately the same distance from the
heterologous transcription start site as it is from the
transcription start site in its natural setting. As is known in the
art, however, some variation in this distance can be accommodated
without loss of promoter function.
[0114] Polyadenylation sequences can also be added to the
expression vector in order to increase the efficiency of Sef mRNA
translation. Two distinct sequence elements are required for
accurate and efficient polyadenylation: GU or U rich sequences
located downstream from the polyadenylation site and a highly
conserved sequence of six nucleotides, AAUAAA, located 11-30
nucleotides upstream. Termination and polyadenylation signals that
are suitable for the present invention include those derived from
SV40.
[0115] In addition to the elements already described, the
expression vector of the present invention may typically contain
other specialized elements intended to increase the level of
expression of cloned nucleic acids or to facilitate the
identification of cells that carry the recombinant DNA. For
example, a number of animal viruses contain DNA sequences that
promote the extra chromosomal replication of the viral genome in
permissive cell types. Plasmids bearing these viral replicons are
replicated episomally as long as the appropriate factors are
provided by genes either carried on the plasmid or with the genome
of the host cell.
[0116] The vector may or may not include a eukaryotic replicon. If
a eukaryotic replicon is present, then the vector is amplifiable in
eukaryotic cells using the appropriate selectable marker. If the
vector does not comprise a eukaryotic replicon, no episomal
amplification is possible. Instead, the recombinant DNA integrates
into the genome of the engineered cell, where the promoter directs
expression of the desired nucleic acid.
[0117] The expression vector of the present invention can further
include additional polynucleotide sequences that allow, for
example, the translation of several proteins from a single mRNA
such as an internal ribosome entry site (IRES) and sequences for
genomic integration of the promoter-chimeric polypeptide.
[0118] Examples for mammalian expression vectors include, but are
not limited to, pcDNA3, pcDNA3. 1(.+-.), pGL3, pZeoSV2(.+-.),
pSecTag2, pDisplay, pEF/myc/cyto, pCMV/myc/cyto, pCR3.1, pSinRep5,
DH26S, DHBB, pNMT1, pNMT41, pNMT81, which are available from
Invitrogen, pCI which is available from Promega, pMbac, ppbac,
pBK-RSV and pBK-CMV which are available from Strategene, pTRES
which is available from Clontech, and their derivatives.
[0119] Expression vectors containing regulatory elements from
eukaryotic viruses such as retroviruses can be also used. SV40
vectors include pSVT7 and pMT2. Vectors derived from bovine
papilloma virus include pBV-1MTHA, and vectors derived from Epstein
Bar virus include pHEBO, and p2O5. Other exemplary vectors include
pMSG, PLNCX (a virus shuttle vector), pAV009/A.sup.+,
pMTO10/A.sup.+, pMAMneo-5, baculovirus pDSVE, and any other vector
allowing expression of proteins under the direction of the SV-40
early promoter, SV-40 late promoter, metallothionein promoter,
murine mammary tumor virus promoter, Rous sarcoma virus promoter,
polyhedrin promoter, or other promoters shown effective for
expression in eukaryotic cells.
[0120] As described above, viruses are very specialized infectious
agents that have evolved, in many cases, to elude host defense
mechanisms. Typically, viruses infect and propagate in specific
cell types. The targeting specificity of viral vectors utilizes its
natural specificity to specifically target predetermined cell types
and thereby introduce a recombinant gene into the infected cell.
Thus, the type of vector used by the present invention will depend
on the cell type transformed. The ability to select suitable
vectors according to the cell type transformed is well within the
capabilities of the ordinary skilled artisan and as such no general
description of selection consideration is provided herein. For
example, kidney cells may be targeted using the heterologous
promoter present in the baculovirus Autographa californica
nucleopolyhedrovirus (AcMNPV) as described in Liang C Y et al.,
2004 (Arch Virol. 149: 51-60) and ovarian cancer cells may be
targeted using a recombinant adeno-associated virus-2 (rAAV) as
described by Mahendra G, et al. [Cancer Gene Ther. Sep. 10, 2004,
Epub ahead of print, 2005 January;12(1):26-34].
[0121] Recombinant viral vectors are useful for in vivo expression
of Sef since they offer advantages such as lateral infection and
targeting specificity. Lateral infection is inherent in the life
cycle of, for example, retrovirus and is the process by which a
single infected cell produces many progeny virions that bud off and
infect neighboring cells. The result is that a large area becomes
rapidly infected, most of which was not initially infected by the
original viral particles. This is in contrast to vertical-type of
infection in which the infectious agent spreads only through
daughter progeny. Viral vectors can also be produced that are
unable to spread laterally. This characteristic can be useful if
the desired purpose is to introduce a specified gene into only a
localized number of targeted cells.
[0122] Various methods can be used to introduce the expression
vector of the present invention into the targeted cells (i.e., the
cancerous cells of the solid tumor). Such methods are generally
described in Sambrook et al., Molecular Cloning: A Laboratory
Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in
Ausubel et al., Current Protocols in Molecular Biology, John Wiley
and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene
Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene
Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of
Molecular Cloning Vectors and Their Uses, Butterworths, Boston
Mass. (1988) and Gilboa et at. [Biotechniques 4 (6): 504-512, 1986]
and include, for example, stable or transient transfection,
lipofection, electroporation and infection with recombinant viral
vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992
for positive-negative selection methods.
[0123] Introduction of nucleic acids by viral infection offers
several advantages over other methods such as lipofection and
electroporation, since higher transfection efficiency can be
obtained due to the infectious nature of viruses.
[0124] An agent capable of upregulating Sef may also be any
compound which is capable of increasing the transcription and/or
translation of an endogenous DNA or mRNA encoding the Sef
polypeptide and thus increasing endogenous Sef activity. For
example, FGF was found to increase Sef transcripts in chick embryos
(data not shown and Ron D., ASBMB annual meeting, Boston, Jun.
12-16, 2004). In addition, as determined by RT-PCR analysis,
various hormones such as FSH and LH-like hormones are capable of
upregulating Sef transcription in mice ovary (data not shown). It
will be appreciated that many other hormones or growth factors such
as androgens, TSH, PDGF, NGF, insulin, and/or VEGF are highly
likely to upregulate Sef transcription, RNA stability, translation
and/or activity.
[0125] Thus, according to preferred embodiments of the present
invention, the upregulating agent used by the present invention a
growth factor and/or a regulating hormone.
[0126] An agent capable of upregulating Sef may also be an
exogenous polypeptide including at least a functional portion (as
described hereinabove) of the Sef protein. Methods of identifying
such exogenous polypeptides are known in the art (Torii S, et al.,
2004; Developmental Cell 7: 33-44; Tsang et al., 2002).
[0127] Upregulation of Sef can be also achieved by introducing to
the subject at least one Sef substrate. Non-limiting examples of
such agents include hormones such as FSH and LH which can be
administered orally, intravenously or locally directly to the tumor
tissue to thereby upregulate Sef expression level and/or activity
within specific tumor cells.
[0128] It will be appreciated that since FGFR is expressed in many
types of tumors, FGF and Sef (or an expression vector encoding
same) can be co-administered to the subject to facilitate and/or
improve Sef activity in reducing and/or inhibiting tumor
growth.
[0129] It will be appreciated that the differential expression of
the various hSef isoforms (see Examples 2 and 6 of the Examples
section which follows) may suggest the use of tissue-specific Sef
isoforms for the inhibition of tissue-specific tumor growth. For
example, upregulation of hSef-b in a tissue where it is usually not
expressed (e.g., adrenal or ovary) or moderately expressed (e.g.,
testes) can lead to efficient inhibition of tumor growth and
subsequent treatment of the cancer and/or cancer metastases.
[0130] Each of the upregulating agents described hereinabove or the
expression vector encoding Sef or a functional portion thereof can
be administered to the individual per se or as part of a
pharmaceutical composition which also includes a physiologically
acceptable carrier. The purpose of a pharmaceutical composition is
to facilitate administration of the active ingredient to an
organism.
[0131] As used herein a "pharmaceutical composition" refers to a
preparation of one or more of the active ingredients described
herein with other chemical components such as physiologically
suitable carriers and excipients. The purpose of a pharmaceutical
composition is to facilitate administration of a compound to an
organism.
[0132] Herein the term "active ingredient" refers to the
upregulating agent or the expression vector encoding Sef or a
functional portion thereof which are accountable for the biological
effect.
[0133] Hereinafter, the phrases "physiologically acceptable
carrier" and "pharmaceutically acceptable carrier" which may be
interchangeably used refer to a carrier or a diluent that does not
cause significant irritation to an organism and does not abrogate
the biological activity and properties of the administered
compound. An adjuvant is included under these phrases.
[0134] Herein the term "excipient" refers to an inert substance
added to a pharmaceutical composition to further facilitate
administration of an active ingredient. Examples, without
limitation, of excipients include calcium carbonate, various sugars
and types of starch, cellulose derivatives, gelatin, vegetable oils
and polyethylene glycols.
[0135] Techniques for formulation and administration of drugs may
be found in "Remington's Pharmaceutical Sciences," Mack Publishing
Co., Easton, Pa., latest edition, which is incorporated herein by
reference.
[0136] Suitable routes of administration may, for example, include
oral, rectal, transmucosal, especially transnasal, intestinal or
parenteral delivery, including intramuscular, subcutaneous and
intramedullary injections as well as intrathecal, direct
intraventricular, intravenous, inrtaperitoneal, intranasal, or
intraocular injections.
[0137] Alternately, one may administer the pharmaceutical
composition in a local rather than systemic manner, for example,
via injection of the pharmaceutical composition directly into a
tissue region of a patient.
[0138] Pharmaceutical compositions of the present invention may be
manufactured by processes well known in the art, e.g., by means of
conventional mixing, dissolving, granulating, dragee-making,
levigating, emulsifying, encapsulating, entrapping or lyophilizing
processes.
[0139] Pharmaceutical compositions for use in accordance with the
present invention thus may be formulated in conventional manner
using one or more physiologically acceptable carriers comprising
excipients and auxiliaries, which facilitate processing of the
active ingredients into preparations which, can be used
pharmaceutically. Proper formulation is dependent upon the route of
administration chosen.
[0140] For injection, the active ingredients of the pharmaceutical
composition may be formulated in aqueous solutions, preferably in
physiologically compatible buffers such as Hank's solution,
Ringer's solution, or physiological salt buffer. For transmucosal
administration, penetrants appropriate to the barrier to be
permeated are used in the formulation. Such penetrants are
generally known in the art.
[0141] For oral administration, the pharmaceutical composition can
be formulated readily by combining the active compounds with
pharmaceutically acceptable carriers well known in the art. Such
carriers enable the pharmaceutical composition to be formulated as
tablets, pills, dragees, capsules, liquids, gels, syrups, slurries,
suspensions, and the like, for oral ingestion by a patient.
Pharmacological preparations for oral use can be made using a solid
excipient, optionally grinding the resulting mixture, and
processing the mixture of granules, after adding suitable
auxiliaries if desired, to obtain tablets or dragee cores. Suitable
excipients are, in particular, fillers such as sugars, including
lactose, sucrose, mannitol, or sorbitol; cellulose preparations
such as, for example, maize starch, wheat starch, rice starch,
potato starch, gelatin, gum tragacanth, methyl cellulose,
hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or
physiologically acceptable polymers such as polyvinylpyrrolidone
(PVP). If desired, disintegrating agents may be added, such as
cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt
thereof such as sodium alginate.
[0142] Dragee cores are provided with suitable coatings. For this
purpose, concentrated sugar solutions may be used which may
optionally contain gum arabic, talc, polyvinyl pyrrolidone,
carbopol gel, polyethylene glycol, titanium dioxide, lacquer
solutions and suitable organic solvents or solvent mixtures.
Dyestuffs or pigments may be added to the tablets or dragee
coatings for identification or to characterize different
combinations of active compound doses.
[0143] Pharmaceutical compositions which can be used orally,
include push-fit capsules made of gelatin as well as soft, sealed
capsules made of gelatin and a plasticizer, such as glycerol or
sorbitol. The push-fit capsules may contain the active ingredients
in admixture with filler such as lactose, binders such as starches,
lubricants such as talc or magnesium stearate and, optionally,
stabilizers. In soft capsules, the active ingredients may be
dissolved or suspended in suitable liquids, such as fatty oils,
liquid paraffin, or liquid polyethylene glycols. In addition,
stabilizers may be added. All formulations for oral administration
should be in dosages suitable for the chosen route of
administration.
[0144] For buccal administration, the compositions may take the
form of tablets or lozenges formulated in conventional manner.
[0145] For administration by nasal inhalation, the active
ingredients for use according to the present invention are
conveniently delivered in the form of an aerosol spray presentation
from a pressurized pack or a nebulizer with the use of a suitable
propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane,
dichloro-tetrafluoroethane or carbon dioxide. In the case of a
pressurized aerosol, the dosage unit may be determined by providing
a valve to deliver a metered amount. Capsules and cartridges of,
e.g., gelatin for use in a dispenser may be formulated containing a
powder mix of the compound and a suitable powder base such as
lactose or starch.
[0146] The pharmaceutical composition described herein may be
formulated for parenteral administration, e.g., by bolus injection
or continuous infusion. Formulations for injection may be presented
in unit dosage form, e.g., in ampoules or in multidose containers
with optionally, an added preservative. The compositions may be
suspensions, solutions or emulsions in oily or aqueous vehicles,
and may contain formulatory agents such as suspending, stabilizing
and/or dispersing agents.
[0147] Pharmaceutical compositions for parenteral administration
include aqueous solutions of the active preparation in
water-soluble form. Additionally, suspensions of the active
ingredients may be prepared as appropriate oily or water based
injection suspensions. Suitable lipophilic solvents or vehicles
include fatty oils such as sesame oil, or synthetic fatty acids
esters such as ethyl oleate, triglycerides or liposomes. Aqueous
injection suspensions may contain substances, which increase the
viscosity of the suspension, such as sodium carboxymethyl
cellulose, sorbitol or dextran. Optionally, the suspension may also
contain suitable stabilizers or agents which increase the
solubility of the active ingredients to allow for the preparation
of highly concentrated solutions.
[0148] Alternatively, the active ingredient may be in powder form
for constitution with a suitable vehicle, e.g., sterile,
pyrogen-free water based solution, before use.
[0149] The pharmaceutical composition of the present invention may
also be formulated in rectal compositions such as suppositories or
retention enemas, using, e.g., conventional suppository bases such
as cocoa butter or other glycerides.
[0150] Pharmaceutical compositions suitable for use in context of
the present invention include compositions wherein the active
ingredients are contained in an amount effective to achieve the
intended purpose. More specifically, a therapeutically effective
amount means an amount of active ingredients (the upregulating
agent or the expression vector encoding Sef) effective to prevent,
alleviate or ameliorate symptoms of a disorder (e.g., inhibit tumor
growth) or prolong the survival of the subject being treated.
[0151] Determination of a therapeutically effective amount is well
within the capability of those skilled in the art, especially in
light of the detailed disclosure provided herein.
[0152] For any preparation used in the methods of the invention,
the therapeutically effective amount or dose can be estimated
initially from in vitro and cell culture assays. For example, a
dose can be formulated in animal models to achieve a desired
concentration or titer. Such information can be used to more
accurately determine useful doses in humans.
[0153] Toxicity and therapeutic efficacy of the active ingredients
described herein can be determined by standard pharmaceutical
procedures in vitro, in cell cultures or experimental animals. The
data obtained from these in vitro and cell culture assays and
animal studies can be used in formulating a range of dosage for use
in human. The dosage may vary depending upon the dosage form
employed and the route of administration utilized. The exact
formulation, route of administration and dosage can be chosen by
the individual physician in view of the patient's condition (See
e.g., Fingl, et al., 1975, in "The Pharmacological Basis of
Therapeutics", Ch. 1 p. 1).
[0154] Dosage amount and interval may be adjusted individually to
provide plasma levels of the active ingredient are sufficient to
inhibit tumor growth (minimal effective concentration, MEC). The
MEC will vary for each preparation, but can be estimated from in
vitro data. Dosages necessary to achieve the MEC will depend on
individual characteristics and route of administration. Detection
assays can be used to determine plasma concentrations.
[0155] Depending on the severity and responsiveness of the
condition to be treated, dosing can be of a single or a plurality
of administrations, with course of treatment lasting from several
days to several weeks or until cure is effected or diminution of
the disease state is achieved.
[0156] The amount of a composition to be administered will, of
course, be dependent on the subject being treated, the severity of
the affliction, the manner of administration, the judgment of the
prescribing physician, etc.
[0157] Compositions of the present invention may, if desired, be
presented in a pack or dispenser device, such as an FDA approved
kit, which may contain one or more unit dosage forms containing the
active ingredient. The pack may, for example, comprise metal or
plastic foil, such as a blister pack. The pack or dispenser device
may be accompanied by instructions for administration. The pack or
dispenser may also be accommodated by a notice associated with the
container in a form prescribed by a governmental agency regulating
the manufacture, use or sale of pharmaceuticals, which notice is
reflective of approval by the agency of the form of the
compositions or human or veterinary administration. Such notice,
for example, may be of labeling approved by the U.S. Food and Drug
Administration for prescription drugs or of an approved product
insert. Compositions comprising a preparation of the invention
formulated in a compatible pharmaceutical carrier may also be
prepared, placed in an appropriate container, and labeled for
treatment of an indicated condition, as if further detailed
above.
[0158] Thus, the teachings of the present invention can be used to
treat individuals having a cancerous tumor (e.g., a solid tumor in
the kidney) and/or a cancerous metastases. For example, an
expression vector (e.g., a viral vector) including a polynucleotide
sequence encoding the human Sef-b mRNA (SEQ ID NO:4) and the
suitable promoter sequences to enable expression in kidney cells is
introduced into the individual via intravenous administration.
Expression of such a vector in the kidney is expected to upregulate
the expression level and/or activity of Sef in this tissue and thus
to inhibit FGF and/or PDGF-induced cell proliferation in the tumor
cells. Dosage of such an expression vector should be calibrated
using cell culture experiments and animal models. Success of
treatment is preferably evaluated by determining the tumor size
(using for example C.T. scans) and the individual general health
status.
[0159] It will be appreciated, that if such a treatment is employed
early following the detection of a cancerous tumor, it may prevent
the complications associated with tumor growth (e.g., metastases)
and thus improve the individual's prognosis and quality of
life.
[0160] It will be appreciated that the agent of the present
invention (which increases the transcription, translation and/or
activity of Sef), can be identified using a variety of methods
known in the art. For example, cells expressing low levels of
endogenous Sef (e.g., NIH 3T3 cells) can be cultured in 10-cm
dishes in the presence of a culture medium (e.g., DMEM medium)
supplemented with serum (e.g., 10% newborn calf serum). To identify
a potential agent which upregulates the transcription, translation
and/or activity of Sef, various transcription factors, drugs and
molecules such as hormones (e.g., FSH and LH-like hormones) can be
added to the culture medium for an incubation period which is
expected to cause upregulation of transcription, translation and
activity. As is shown in FIGS. 9a-b, such incubation period can
vary between minutes to hours, and it is within the capabilities of
those skilled in the art to determine the suitable incubation
periods.
[0161] Since the functional portion of Sef is included in the
intracellular fraction (see Example 1 of the Examples section which
follows), the effect of the agent on Sef expression levels and/or
activity of Sef is preferably determined by analyzing the cells and
not the cell medium. Thus, the cells are collected and centrifuged,
the medium is discarded and the cell pellet is further subjected to
RNA and/or protein detection methods.
[0162] Alternatively, the anti-mitogenic activity of Sef (see
Example 3 of the Examples section which follows) can be measured by
determining the level of DNA synthesis in such cells (a mitogenic
assay), or counting cell number as a measure for Sef effect on
proliferation.
[0163] Following is a list of methods useful for detecting Sef RNA
level in cells.
[0164] Northern Blot analysis: This method involves the detection
of a particular RNA in a mixture of RNAs. An RNA sample is
denatured by treatment with an agent (e.g., formaldehyde) that
prevents hydrogen bonding between base pairs, ensuring that all the
RNA molecules have an unfolded, linear conformation. The individual
RNA molecules are then separated according to size by gel
electrophoresis and transferred to a nitrocellulose or a
nylon-based membrane to which the denatured RNAs adhere. The
membrane is then exposed to labeled DNA probes. Probes may be
labeled using radio-isotopes or enzyme linked nucleotides.
Detection may be using autoradiography, colorimetric reaction or
chemiluminescence. This method allows both quantitation of an
amount of particular RNA molecules and determination of its
identity by a relative position on the membrane which is indicative
of a migration distance in the gel during electrophoresis.
[0165] RT-PCR analysis: This method uses PCR amplification of
relatively rare RNAs molecules. First, RNA molecules are purified
from the cells and converted into complementary DNA (cDNA) using a
reverse transcriptase enzyme (such as an MMLV-RT) and primers such
as, oligo dT, random hexamers or gene specific primers. Then by
applying gene specific primers [e.g., the forward and reverse
hSef-b primers (SEQ ID NOs:2 and 1, respectively)] and Taq DNA
polymerase, a PCR amplification reaction is carried out in a PCR
machine. Those of skills in the art are capable of selecting the
length and sequence of the gene specific primers and the PCR
conditions (i.e., annealing temperatures, number of cycles and the
like) which are suitable for detecting specific RNA molecules. It
will be appreciated that a semi-quantitative RT-PCR reaction can be
employed by adjusting the number of PCR cycles and comparing the
amplification product to known controls.
[0166] RNA in situ hybridization stain: In this method DNA or RNA
probes are attached to the RNA molecules present in the cells.
Generally, the cells are first fixed to microscopic slides to
preserve the cellular structure and to prevent the RNA molecules
from being degraded and then are subjected to hybridization buffer
containing the labeled probe. The probe can be for example an
RNA-oligonucleotide probe (e.g., a 5'-biotinylated 2-O-methyl RNA
oligonucleotide) which is synthesized according to a selected
sequence from the unique 5' region of hSef-b (i.e., nucleic acids
1-240 as set forth in SEQ ID NO:7). The hybridization buffer
includes reagents such as formamide and salts (e.g., sodium
chloride and sodium citrate) which enable specific hybridization of
the DNA or RNA probes with their target mRNA molecules in situ
while avoiding non-specific binding of probe. Those of skills in
the art are capable of adjusting the hybridization conditions
(i.e., temperature, concentration of salts and formamide and the
like) to specific probes and types of cells. Following
hybridization, any unbound probe is washed off and the slide is
subjected to either a photographic emulsion which reveals signals
generated using radio-labeled probes or to a colorimetric reaction
which reveals signals generated using enzyme-linked labeled
probes.
[0167] In situ RT-PCR stain: This method is described in Nuovo G J,
et al. [Intracellular localization of polymerase chain reaction
(PCR)-amplified hepatitis C cDNA. Am J Surg Pathol. 1993, 17:
683-90] and Komminoth P, et al. [Evaluation of methods for
hepatitis C virus detection in archival liver biopsies. Comparison
of histology, immunohistochemistry, in situ hybridization, reverse
transcriptase polymerase chain reaction (RT-PCR) and in situ
RT-PCR. Pathol Res Pract. 1994, 190: 1017-25]. Briefly, the RT-PCR
reaction is performed on fixed cells by incorporating labeled
nucleotides to the PCR reaction. The reaction is carried on using a
specific in situ RT-PCR apparatus such as the laser-capture
microdissection PixCell I LCM system available from Arcturus
Engineering (Mountainview, Calif.).
[0168] Oligonucleotide microarray: In this method oligonucleotide
probes capable of specifically hybridizing with the polynucleotides
of the present invention (i.e., human Sef RNA) are attached to a
solid surface (e.g., a glass wafer). Each oligonucleotide probe is
of approximately 20-25 nucleic acids in length. To detect the
expression pattern of the polynucleotides of the present invention
in a specific tissue sample (e.g., a breast tissue), RNA is
extracted from the tissue sample using methods known in the art
(using e.g., a TRIZOL solution, Gibco BRL, USA). Hybridization can
take place using either labeled oligonucleotide probes (e.g.,
5'-biotinylated probes) or labeled fragments of complementary DNA
(cDNA) or RNA (cRNA). Briefly, double stranded cDNA is prepared
from the RNA using reverse transcriptase (RT) (e.g., Superscript II
RT), DNA ligase and DNA polymerase I, all according to
manufacturer's instructions (Invitrogen Life Technologies,
Frederick, Md., USA). To prepare labeled cRNA, the double stranded
cDNA is subjected to an in vitro transcription reaction in the
presence of biotinylated nucleotides using e.g., the BioArray High
Yield RNA Transcript Labeling Kit (Enzo, Diagnostics, Affymetix
Santa Clara Calif.). For efficient hybridization the labeled cRNA
can be fragmented by incubating the RNA in 40 mM Tris Acetate (pH
8.1), 100 mM potassium acetate and 30 mM magnesium acetate for 35
minutes at 94.degree. C. Following hybridization, the microarray is
washed and the hybridization signal is scanned using a confocal
laser fluorescence scanner which measures fluorescence intensity
emitted by the labeled cRNA bound to the probe arrays.
[0169] For example, in the Affymetrix microarray (Affymetrix.RTM.,
Santa Clara, Calif.) each gene on the array is represented by a
series of different oligonucleotide probes, of which, each probe
pair consists of a perfect match oligonucleotide and a mismatch
oligonucleotide. While the perfect match probe has a sequence
exactly complimentary to the particular gene, thus enabling the
measurement of the level of expression of the particular gene, the
mismatch probe differs from the perfect match probe by a single
base substitution at the center base position. The hybridization
signal is scanned using the Agilent scanner, and the Microarray
Suite software subtracts the non-specific signal resulting from the
mismatch probe from the signal resulting from the perfect match
probe.
[0170] Following is a list of immunological detection methods which
can be used to detect the level of Sef protein in cells.
[0171] Enzyme linked immunosorbent assay (ELISA): This method
involves fixation of a sample (e.g., fixed cells or a proteinaceous
solution) containing a protein substrate to a surface such as a
well of a microtiter plate. A substrate specific antibody coupled
to an enzyme is applied and allowed to bind to the substrate.
Presence of the antibody is then detected and quantitated by a
colorimetric reaction employing the enzyme coupled to the antibody.
Enzymes commonly employed in this method include horseradish
peroxidase and alkaline phosphatase. If well calibrated and within
the linear range of response, the amount of substrate present in
the sample is proportional to the amount of color produced. A
substrate standard is generally employed to improve quantitative
accuracy.
[0172] Western blot: This method involves separation of a substrate
from other protein by means of an acrylamide gel followed by
transfer of the substrate to a membrane (e.g., nylon or PVDF).
Presence of the substrate is then detected by antibodies specific
to the substrate, which are in turn detected by antibody binding
reagents. Antibody binding reagents may be, for example, protein A,
or other antibodies. Antibody binding reagents may be radiolabeled
or enzyme linked as described hereinabove. Detection may be by
autoradiography, colorimetric reaction or chemiluminescence. This
method allows both quantitation of an amount of substrate and
determination of its identity by a relative position on the
membrane which is indicative of a migration distance in the
acrylamide gel during electrophoresis. In addition, using
phospho-specific antibodies, this method allows the determination
of the activation state of specific proteins [e.g., P-p38 or
P-ERK1/2 (see Example 4 of the Examples section which
follows)].
[0173] Radio-immunoassay (RIA): In one version, this method
involves precipitation of the desired protein (i.e., the substrate)
with a specific antibody and radiolabeled antibody binding protein
(e.g., protein A labeled with I.sup.125) immobilized on a
precipitable carrier such as agarose beads. The number of counts in
the precipitated pellet is proportional to the amount of
substrate.
[0174] In an alternate version of the RIA, a labeled substrate and
an unlabelled antibody binding protein are employed. A sample
containing an unknown amount of substrate is added in varying
amounts. The decrease in precipitated counts from the labeled
substrate is proportional to the amount of substrate in the added
sample.
[0175] Fluorescence activated cell sorting (FACS): This method
involves detection of a substrate in situ in cells by substrate
specific antibodies. The substrate specific antibodies are linked
to fluorophores. Detection is by means of a cell sorting machine
which reads the wavelength of light emitted from each cell as it
passes through a light beam. This method may employ two or more
antibodies simultaneously.
[0176] Immunohistochemical analysis: This method involves detection
of a substrate (i.e., Sef) in situ in fixed cells by substrate
specific antibodies. The substrate specific antibodies may be
enzyme linked or linked to fluorophores. Detection is by microscopy
and subjective or automatic evaluation. If enzyme linked antibodies
are employed, a colorimetric reaction may be required. It will be
appreciated that immunohistochemistry is often followed by
counterstaining of the cell nuclei using for example Hematoxyline
or Giemsa stain.
[0177] It will be appreciated that Sef activity (i.e., inhibition
of RTK ligand-induced proliferation and/or downregulation of the
over-expressed RTK receptors via the inhibition of P-ERK1/2) can be
detected as described in details in Examples 3-5 of the Examples
section which follows.
[0178] Thus, the agent of which addition to the cells results in
upregulation of the expression level and/or activity of endogenous
Sef in the cells is identified as a potential upregulating agent
and can be used to inhibit tumor growth in the subject.
[0179] As is mentioned hereinabove and is described in Example 8 of
the Examples section which follows, hSef expression was
significantly downregulated and/or completely lost in various solid
cancerous tumors, in a manner which correlates with tumor
invasiveness and/or malignancy. Thus, a decrease in the expression
level of hSef in a tissue of a solid tumor as compared to a normal,
unaffected tissue (i.e., devoid of cancer) which is derived from
either an unaffected subject or from the same subject in need of
diagnosis (e.g., a mammary tissue devoid of cancer) can be used to
determine the presence and/or degree of malignancy of solid tumors
and thus diagnose cancer.
[0180] Thus, according to another aspect of the present invention
there is provided a method of diagnosing cancer in a subject in
need thereof. The method is effected by detecting in a tissue
sample of the subject an expression level of Sef, wherein a
decrease in the expression level of the Sef compared to the
expression level of the Sef in an unaffected tissue sample is
indicative of the cancer, thereby diagnosing the cancer in the
subject.
[0181] As used herein the term "diagnosing" refers to classifying a
disease or a symptom, determining a severity of the disease,
monitoring disease progression, forecasting an outcome of a disease
and/or prospects of recovery. Preferably, the term "diagnosing" as
used herein also encompasses determining a malignancy of the solid
tumor, e.g., determining course of disease, cancer staging,
invasiveness and/or metastatic stage (e.g., presence or absence of
cancer metastases). It will be appreciated that determining the
course of disease (e.g., a highly malignant cancer which develops
fast or a slow growing cancer) as well as forcasting the outcome of
the disease (e.g., prognosis) can be used to determine the type
and/or dosage i.e., regimen of the anti-cancer therapy used to
treat the subject in need.
[0182] For example, a significant downregulation of Sef expression
(e.g., a complete loss of Sef expression) in a relatively
small-size tumor (e.g., a breast tumor of less than 0.5-1 cm) may
indicate the presence of highly malignant and/or highly aggressive
cancerous cells which may result in a fast growing tumor and/or
highly metastatic cancer. On the other hand, a moderate
downregulation of Sef expression in a moderate-size tumor may
indicate the presence of a less aggressive, slow growing cancer.
Additionally or alternatively, downregulation of Sef in cancerous
cells along with overexpression of an oncogene such as c-erb,
and/or downregulation of the expression level of another tumor
suppressor gene may indicate the degree of cancer malignancy and/or
aggressiveness. Thus, the choice of treatment can be selected
according to the degree of malignancy and/or aggressiveness of
cancer as determined by Sef expression alone and/or in comination
with other known cancer diagnostic markers (e.g., HER-2, P53, ER,
PR).
[0183] As used herein the phrase a "subject in need thereof" refers
to a mammal, preferably a human being (male or female) at any age
which is in need of diagnosis of a solid tumor. Such a subject can
be predisposed to develop a solid tumor due to a mutation in an
oncogene or a tumor suppressor (e.g., a carrier of a mutation in
BRCA1, BRCA2, P53), family history of cancer (e.g., having a first
degree relative with cancer) and/or exposure to environmental
hazard (e.g., DNA damaging agents, carcinogens, irradiation).
Additionally or alternatively, such a subject is suspected to have
a solid tumor based on abnormal physical findings (e.g., a
suspicious lump, a cyst and the like) observed using endoscopy
(e.g., colonoscopy), physical examination and/or a suspicious
imaging finding (e.g., obtained by ultrasound, X-ray, CT scan or
MRI).
[0184] The cancer which is diagnosed by the method according to
this aspect of the present invention can be any type of cancer in
which Sef expression is downregulated. Non-limiting examples of
cancers which can be diagnosed according to the method of this
aspect of the present invention include cancer of epithelial
origin, cancer of mesenchymal origin (e.g., sarcoma) or cancer of
the nervous system (e.g., brain tumor, glial and astrocyte tumors).
For example, such a cancer can be breast cancer, ovarian cancer,
thyroid carcinoma, prostate cancer, brain cancer, colon cancer,
skin cancer, pancreatic cancer, endometrial carcinoma, adrenal
carcinoma, pituitary cancer, tonsillar carcinoma, spleen cancer,
adenoids cancer, kidney cancer, liver cancer, testis cancer,
bladder cancer, bile duct, lung cancer and stomach cancer.
[0185] Preferably, the cancer is a solid tumor cancer. It will be
appreciated that the solid tumor can be a primary solid tumor
(i.e., a tumor which is located in the place where the cancer
started) as well as a secondary solid tumor [i.e., a tumor that
forms as a result of spread (metastasis) of cancer from its site of
origin].
[0186] The phrase "tissue sample" as used herein refers to any
sample of a tissue derived from a subject (e.g., a tissue in which
cancer is suspected), including but not limited to, for example, a
mammary tissue (breast tissue), an ovary tissue, a thyroid tissue,
a prostate tissue, as well as other tissues such as a brain tissue,
a skin tissue or colon tissue. The sample of the tissue can be a
tissue biopsy, fine needle aspiration and/or core needle biopsy
which can be derived by any known surgical mean such as using a
scalpel or a needle.
[0187] As used herein the phrase "unaffected tissue sample" refers
to a tissue sample of the same type as the test tissue (i.e., a
tissue which is subject to diagnosis according to the method of the
present invention, e.g., with a suspected solid tumor) which is
devoid of any solid tumor. Such a tissue sample can be derived from
a healthy, unaffected individual or from the same subject however
from a healthy tissue. For example, if a mammary tissue derived
from a left breast of a female is suspected to have a solid tumor,
the unaffected tissue sample can be a mammary tissue derived from
the right breast of the same female subject. Additionally or
alternatively, the unaffected tissue can be derived from the same
breast of the suspected tumor but from a location that is suspected
to be free of cancer cells.
[0188] As is shown in FIGS. 4a-c and 15a-c and is described in
Examples 2 and 8 of the Examples section which follows, human Sef
splice isoforms exhibit a tissue specific expression pattern. Thus,
while human Sef-a is highly expressed in normal human breast,
brain, pituitary, tonsils, spleen, adenoids, fetal kidney, liver,
testes and ovary, and moderately expressed in primary aortic
endothelial cells, human umbilical vein endothelial cells (HUVEC)
and adrenal medulla; human Sef-b is highly expressed in thyroid and
testes; moderately expressed in pituitary, fetal brain and HUVEC
cells and not expressed (negative) in normal human breast tissue.
As the pattern of expression is known, a reduction of the
expression level of a specific Sef isoform may indicate the
presence of cancer. For example, a decrease in the expression level
of human Sef-a in a breast tissue or an ovary tissue of the subject
who is suspected to have cancer is indicative of the diagnosis of
cancer in the subject. Similarly, a decrease in the expression
level of human Sef-b in a thyroid tissue of the subject who is
suspected to have cancer is indicative of the diagnosis of cancer
in the subject.
[0189] Diagnosis of the cancer (e.g., solid tumor) according to the
method of this aspect of the present invention is performed by
detecting a decrease in the expression level of Sef in a tissue
sample of the subject. Such a decrease can be in the Sef amino acid
sequence of the tissue (e.g., the amino acid sequence as set forth
by SEQ ID NO:5 or 6) or in the Sef nucleic acid sequence of the
tissue (e.g., the nucleic acid sequence as set forth by SEQ ID
NO:4, 8, 9 or 10). Detecting the expression level of Sef can be
performed using any RNA detection method and/or a protein detection
method. Non-limiting examples of RNA detection methods which can be
used along with the method of this aspect of the present invention
include Northern blot analysis, RT-PCR, RNA in situ hybridization,
in situ RT-PCR and RNA microarrays as further described hereinabove
and in the Examples section which follows. Non-limiting examples of
protein detection methods which can be used along with the method
of this aspect of the present invention include Western blot
analysis, immunohistochemistry, immunofluorescence, radio immuno
assay and FACS analysis as further described hereinabove.
[0190] It will be appreciated that prior to detecting the
expression level of Sef in the tissue sample, the tissue sample is
preferably processed and treated according to the desired detection
method. For example, for in situ (i.e., within the cell or tissue
where Sef is naturally expressed) detection of Sef expression level
(using e.g., RNA in situ hybridization, in situ RT-PCR,
immunohistochemistry or immunofluorescence), the tissue sample is
preferably processed to enable tissue sectioning (e.g.,
paraffin-embedded sections, cryosections). Such processing may
include, fixation (e.g., using formaline, paraformaldehyde),
treatment with various agents which facilitate detection of nucleic
acids in the tissue (e.g., hydrogen peroxide, proteases such as
proteinase K) or with agents facilitating detection of specific
polypeptides while preventing non-specific binding of antibodies
(e.g., anti-Sef antibody) to the tissue sample (e.g., by blocking
the tissue with a blocking agent such as serum, milk).
Alternatively, detection of Sef expression level can be performed
on isolated nucleic acid sequences (i.e., RNA molecules, e.g.,
mRNA) or proteins which are extracted from the tissue. It will be
appreciated that for such applications the tissue is preferably a
freshly obtained, non-fixed tissue. Methods of extracting RNA or
proteins from tissue samples are well known in the art.
[0191] Preferably, detection of Sef nucleic acid sequence (using
any of the RNA detection methods described hereinabove) can be
performed using a reagent such as an isolated nucleic acid sequence
capable of specifically hybridizable to Sef nucleic acid sequence
[e.g., a nucleic acid sequence which is complementary (i.e., by
means of hydrogen bonding] to the nucleic acid sequence of Sef). A
non-limiting example of such an isolated nucleic acid sequence is
described in Example 8 of the Examples section which follows and is
set forth by SEQ ID NO:31.
[0192] The term "isolated nucleic acid sequence" includes
oligonucleotides composed of naturally-occurring bases, sugars and
covalent internucleoside linkages (e.g., backbone) as well as
oligonucleotides having non-naturally-occurring portions which
function similarly to respective naturally-occurring portions.
[0193] Oligonucleotides designed according to the teachings of the
present invention can be generated according to any oligonucleotide
synthesis method known in the art such as enzymatic synthesis or
solid phase synthesis. Equipment and reagents for executing
solid-phase synthesis are commercially available from, for example,
Applied Biosystems. Any other means for such synthesis may also be
employed; the actual synthesis of the oligonucleotides is well
within the capabilities of one skilled in the art and can be
accomplished via established methodologies as detailed in, for
example, "Molecular Cloning: A laboratory Manual" Sambrook et al.,
(1989); "Current Protocols in Molecular Biology" Volumes I-III
Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in
Molecular Biology", John Wiley and Sons, Baltimore, Md. (1989);
Perbal, "A Practical Guide to Molecular Cloning", John Wiley &
Sons, New York (1988) and "Oligonucleotide Synthesis" Gait, M. J.,
ed. (1984) utilizing solid phase chemistry, e.g. cyanoethyl
phosphoramidite followed by deprotection, desalting and
purification by for example, an automated trityl-on method or
HPLC.
[0194] Specific examples of preferred oligonucleotides useful
according to this aspect of the present invention include
oligonucleotides containing modified backbones (e.g., those that
retain a phosphorus atom in the backbone) or non-natural
internucleoside linkages, i.e., the backbone, of the nucleotide
units are replaced with novel groups. The base units are maintained
for complementation with the appropriate polynucleotide target. An
example for such an oligonucleotide mimetic, includes peptide
nucleic acid (PNA). A PNA oligonucleotide refers to an
oligonucleotide where the sugar-backbone is replaced with an amide
containing backbone, in particular an aminoethylglycine backbone.
The bases are retained and are bound directly or indirectly to aza
nitrogen atoms of the amide portion of the backbone. United States
patents that teach the preparation of PNA compounds include, but
are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and
5,719,262, each of which is herein incorporated by reference. Other
backbone modifications, which can be used in the present invention
are disclosed in U.S. Pat. No. 6,303,374.
[0195] Oligonucleotides of the present invention may also include
base modifications or substitutions. As used herein, "unmodified"
or "natural" bases include the purine bases adenine (A) and guanine
(G), and the pyrimidine bases thymine (T), cytosine (C) and uracil
(U). Modified bases include but are not limited to other synthetic
and natural bases such as 5-methylcytosine (5-me-C). Further base
modifications include those disclosed in U.S. Pat. No. 3,687,808,
those disclosed in The Concise Encyclopedia Of Polymer Science And
Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley &
Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie,
International Edition, 1991, 30, 613, and those disclosed by
Sanghvi, Y. S., Chapter 15, Antisense Research and Applications,
pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993.
Such bases are particularly useful for increasing the binding
affinity of the oligomeric compounds of the invention. These
include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6
and O-6 substituted purines, including 2-aminopropyladenine,
5-propynyluracil and 5-propynylcytosine. 5-methylcytosine
substitutions have been shown to increase nucleic acid duplex
stability by 0.6-1.2.degree. C. [Sanghvi Y S et al. (1993)
Antisense Research and Applications, CRC Press, Boca Raton 276-278]
and are presently preferred base substitutions, even more
particularly when combined with 2'-O-methoxyethyl sugar
modifications.
[0196] It will be appreciated that the isolated nucleic acid
sequence of the present invention can be of any size, e.g., from
10-40 nucleic acids to about 100-300 nucleic acids or even
1000-3000 nucleic acids in length.
[0197] Preferably, for the specific hybridization of the isolated
nucleic acid sequence with Sef, the isolated nucleic acid sequence
is of at least 25, at least 50, at least 75, at least 100, at least
150, at least 250, at least 350 bases.
[0198] It will be appreciated that for certain detection methods
(e.g., an oligonucleotide microarray as is further described
hereinbelow), the isolated nucleic acid sequence of the present
invention is preferably bound to a solid support, such as a solid
surface (e.g., a glass wafer) as is further described hereinunder.
Usually the solid support is a microsphere (bead), a magnetic bead,
a nitrocellulose membrane, a nylon membrane, a glass slide, a fused
silica (quartz) slide, a gold film, a polypyrrole film, an optical
fiber and/or a microplate well.
[0199] As is further described hereinunder, the isolated nucleic
acid sequence of the present invention can be labeled. Various
methods can be used to label the isolated nucleic acid sequence of
the present invention. These include fluorescent labeling with a
fluorophore conjugated via a linker or a chemical bond to at least
one nucleotide, or the use of a covalently conjugated enzyme (e.g.,
Horse Radish Peroxidase) and a suitable substrate (e.g.,
o-phenylenediamine) which upon interaction therebetween yields a
colorimetric or fluorescent color. Thus, the isolated nucleic acid
sequence can be radiolabeled, Digoxigennin labeled and/or
biotinylated using e.g., in vitro transcription in the presence of
labeled nucleotides.
[0200] Preferably, the expression level of Sef amino acid sequence
can be detected using a protein detection method with an antibody
or antibody fragment which comprises an antigen recognition region
capable of specifically binding to Sef amino acid sequence (e.g.,
as set forth by SEQ ID NO:5 or 6).
[0201] The term "antibody" as used in this invention includes
intact antibody molecules as well as functional fragments thereof,
such as Fab, F(ab')2, Fv or single domain molecules such as VH and
VL to an epitope of an antigen. As used herein, the term "epitope"
refers to any antigenic determinant on an antigen to which the
paratope of an antibody binds. Epitopic determinants usually
consist of chemically active surface groupings of molecules such as
amino acids or carbohydrate side chains and usually have specific
three dimensional structural characteristics, as well as specific
charge characteristics. The functional antibody fragments are
defined as follows: (1) Fab, the fragment which contains a
monovalent antigen-binding fragment of an antibody molecule, can be
produced by digestion of whole antibody with the enzyme papain to
yield an intact light chain and a portion of one heavy chain; (2)
Fab', the fragment of an antibody molecule that can be obtained by
treating whole antibody with pepsin, followed by reduction, to
yield an intact light chain and a portion of the heavy chain; two
Fab' fragments are obtained per antibody molecule; (3) (Fab')2, the
fragment of the antibody that can be obtained by treating whole
antibody with the enzyme pepsin without subsequent reduction;
F(ab')2 is a dimer of two Fab' fragments held together by two
disulfide bonds; (4) Fv, defined as a genetically engineered
fragment containing the variable region of the light chain and the
variable region of the heavy chain expressed as two chains; (5)
Single chain antibody ("SCA"), a genetically engineered molecule
containing the variable region of the light chain and the variable
region of the heavy chain, linked by a suitable polypeptide linker
as a genetically fused single chain molecule; and (6) Single domain
antibodies are composed of a single VH or VL domains which exhibit
sufficient affinity to the antigen.
[0202] Methods of producing polyclonal and monoclonal antibodies as
well as fragments thereof are well known in the art (See for
example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold
Spring Harbor Laboratory, New York, 1988, incorporated herein by
reference).
[0203] Antibody fragments according to the present invention can be
prepared by proteolytic hydrolysis of the antibody or by expression
in E. coli or mammalian cells (e.g. Chinese hamster ovary cell
culture or other protein expression systems) of DNA encoding the
fragment. Antibody fragments can be obtained by pepsin or papain
digestion of whole antibodies by conventional methods. For example,
antibody fragments can be produced by enzymatic cleavage of
antibodies with pepsin to provide a 5S fragment denoted F(ab')2.
This fragment can be further cleaved using a thiol reducing agent,
and optionally a blocking group for the sulfhydryl groups resulting
from cleavage of disulfide linkages, to produce 3.5S Fab'
monovalent fragments. Alternatively, an enzymatic cleavage using
pepsin produces two monovalent Fab' fragments and an Fc fragment
directly. These methods are described, for example, by Goldenberg,
U.S. Pat. Nos. 4,036,945 and 4,331,647, and references contained
therein, which patents are hereby incorporated by reference in
their entirety. See also Porter, R. R. [Biochem. J. 73: 119-126
(1959)]. Other methods of cleaving antibodies, such as separation
of heavy chains to form monovalent light-heavy chain fragments,
further cleavage of fragments, or other enzymatic, chemical, or
genetic techniques may also be used, so long as the fragments bind
to the antigen that is recognized by the intact antibody.
[0204] Fv fragments comprise an association of VH and VL chains.
This association may be noncovalent, as described in Inbar et al.
[Proc. Nat'l Acad. Sci. USA 69:2659-62 (19720]. Alternatively, the
variable chains can be linked by an intermolecular disulfide bond
or cross-linked by chemicals such as glutaraldehyde. Preferably,
the Fv fragments comprise VH and VL chains connected by a peptide
linker. These single-chain antigen binding proteins (sFv) are
prepared by constructing a structural gene comprising DNA sequences
encoding the VH and VL domains connected by an oligonucleotide. The
structural gene is inserted into an expression vector, which is
subsequently introduced into a host cell such as E. coli. The
recombinant host cells synthesize a single polypeptide chain with a
linker peptide bridging the two V domains. Methods for producing
sFvs are described, for example, by Whitlow and Filpula, Methods 2:
97-105 (1991); Bird et al., Science 242:423-426 (1988); Pack et
al., Bio/Technology 11:1271-77 (1993); and U.S. Pat. No. 4,946,778,
which is hereby incorporated by reference in its entirety.
[0205] Another form of an antibody fragment is a peptide coding for
a single complementarity-determining region (CDR). CDR peptides
("minimal recognition units") can be obtained by constructing genes
encoding the CDR of an antibody of interest. Such genes are
prepared, for example, by using the polymerase chain reaction to
synthesize the variable region from RNA of antibody-producing
cells. See, for example, Larrick and Fry [Methods, 2: 106-10
(1991)].
[0206] It will be appreciated that for certain detection methods as
described hereinunder, the antibody or antibody fragment is bound
to a solid support (such as nylon filters, glass slides or silicon
chips) using methods which are well known in the art.
[0207] Preferably, for detecting Sef nucleic acid sequence the
antibody or antibody fragment is labeled (e.g., radiolabeled,
biotinylated or fluorescent labeling) using methods known in the
art.
[0208] The agents of the present invention which are described
hereinabove for detecting expression level of Sef nucleic acid
sequence or amino acid sequence may be included in a diagnostic
kit/article of manufacture preferably along with appropriate
instructions for use and labels indicating FDA approval for use in
diagnosing cancer.
[0209] Such a kit can include, for example, at least one container
including at least one of the above described diagnostic agents
(e.g., reagents such as the isolated nucleic acid sequence and/or
the antibody or antibody fragment) and an imaging reagent packed in
another container (e.g., HRP, alkaline phosphatase,
fluorescently-labeled secondary antibodies, buffers, chromogenic
substrates, fluorogenic material). The kit may also include
appropriate buffers and preservatives for improving the shelf-life
of the kit. Most preferably, the kit can include the addressable
oligonucleotide microarray (DNA chip) described hereinabove.
[0210] Additional objects, advantages, and novel features of the
present invention will become apparent to one ordinarily skilled in
the art upon examination of the following examples, which are not
intended to be limiting. Additionally, each of the various
embodiments and aspects of the present invention as delineated
hereinabove and as claimed in the claims section below finds
experimental support in the following examples.
EXAMPLES
[0211] Reference is now made to the following examples, which
together with the above descriptions, illustrate the invention in a
non limiting fashion.
[0212] Generally, the nomenclature used herein and the laboratory
procedures utilized in the present invention include molecular,
biochemical, microbiological and recombinant DNA techniques. Such
techniques are thoroughly explained in the literature. See, for
example, "Molecular Cloning: A laboratory Manual" Sambrook et al.,
(1989); "Current Protocols in Molecular Biology" Volumes I-III
Ausubel, R. M., Ed. (1994); Ausubel et al., "Current Protocols in
Molecular Biology", John Wiley and Sons, Baltimore, Md. (1989);
Perbal, "A Practical Guide to Molecular Cloning", John Wiley &
Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific
American Books, New York; Birren et al. (Eds.) "Genome Analysis: A
Laboratory Manual Series", Vols. 1-4, Cold Spring Harbor Laboratory
Press, New York (1998); methodologies as set forth in U.S. Pat.
Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057;
"Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E.,
Ed. (1994); "Culture of Animal Cells--A Manual of Basic Technique"
by Freshney, Wiley-Liss, N.Y. (1994), Third Edition; "Current
Protocols in Immunology" Volumes I-III Coligan J. E., Ed. (1994);
Stites et al. (Eds.), "Basic and Clinical Immunology" (8th
Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and
Shiigi (Eds.), "Selected Methods in Cellular Immunology", W. H.
Freeman and Co., New York (1980); available inununoassays are
extensively described in the patent and scientific literature, see,
for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752;
3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074;
3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771
and 5,281,521; "Oligonucleotide Synthesis" Gait, M. J., Ed. (1984);
"Nucleic Acid Hybridization" Hames, B. D., and Higgins S. J., Eds.
(1985); "Transcription and Translation" Hames, B. D., and Higgins
S. J., Eds. (1984); "Animal Cell Culture" Freshney, R. I., Ed.
(1986); "Immobilized Cells and Enzymes" IRL Press, (1986); "A
Practical Guide to Molecular Cloning" Perbal, B., (1984) and
"Methods in Enzymology" Vol. 1-317, Academic Press; "PCR Protocols:
A Guide To Methods And Applications", Academic Press, San Diego,
Calif. (1990); Marshak et al., "Strategies for Protein Purification
and Characterization--A Laboratory Course Manual" CSHL Press
(1996); all of which are incorporated by reference as if fully set
forth herein. Other general references are provided throughout this
document. The procedures therein are believed to be well known in
the art and are provided for the convenience of the reader. All the
information contained therein is incorporated herein by
reference.
[0213] General Material and Experimental Methods
[0214] Enzymes, growth factors, reagents and chemicals--Restriction
enzymes and Taq-polymerases were from NEB (Beverly, Mass.),
Pharmacia (Amersham Pharmacia Biotech LTD, UK) and Roche
(Indianapolis, Ind., USA). Purified recombinant FGF2 was produced
as described (24-26). Bovine brain FGF1, recombinant human FGF4,
epidermal growth factor (EGF) and platelet derived growth factor
(PDGF) were from R&D Systems (R&D Systems Inc, Minneapolis,
Minn., USA). [.sup.35S]-Methionine (1000 Ci/mmol) and
[.sup.3H]-Thymidine (25 Ci/mmole) were from Amersham HVD Biotech.
Fibronectin, fetal and newborn calf serum and media were from
Biological Industries (Beth Ha'emek, Israel, Israel) or
Gibco-Laboratories (Grand Island, N.Y., USA). Fluoromount-GTM was
from Southern Biotechnology Associates, Inc. (Birmingham, Ala.,
USA). BSA was from ICN (UK). All other chemicals were from Sigma
(St Louis, Mo.).
[0215] cDNA cloning and plasmid construction--RT-PCR was utilized
to amplify the entire coding region of hSef-a from human brain or
fibroblast RNA, and of hSef-b from testes RNA. First strand cDNA
was synthesized using the following primer:
5'-AGTGGCAATGCTTAGACTCTTTCGT-3' (SEQ ID NO:1) which is designed
according to the 3' un-translated region (UTR) of a partial hSef
EST clone (GenBank Accession No. AL133097, i.e., a common primer
for both hSef-a and b isoforms). Amplification of the coding region
of hSef-b was performed with nested primer:
5'-GAGGATCCAAGCTTTGTTACAAAGGGGCGACCGCGT-3' (SEQ ID NO:3), and a
primer flanking the amino terminal part unique to the hSef-b
isoform: 5'-GCGTGCCAGACAGAGTGCTAGGCAT-3' (SEQ ID NO:2) which is
designed according to the Testes EST clone GenBank Accession No.
BG72 1995 and is located at the unique 5' sequence of hSef-b
(nucleic acids 126-150 of SEQ ID NO:7; This clone was served as a
platform to reconstruct hSef-a cDNA containing its entire ORF.
Thus, the 5' portion of hSef-a was amplified from human brain or
normal fibroblasts using a primer unique to hSef-a:
5'-GAGGATCCTGACGGCCATGGCCCCGTGGCTGCAGCTC-3' (SEQ ID NO: 16, which
is designed according to the EST clone GenBank Accession No.
BE750478 and is located at the unique 5' sequence of hSef-a
(nucleic acids 1-37 of SEQ ID NO:10), and a primer common to both
Sef isoforms (SEQ ID NO:3). This fragment was digested with BamH1
following sequence verification and ligated to the remainder of
hSef-a sequences. The cDNA of hSef-a or hSef-b was cloned into
pcDNA3.1, pTET splice and pcDNA3.1/myc-His expression vectors
(Invitrogen).
[0216] Analysis of the expression pattern of hsef
transcripts--Total RNA was extracted from human tissues and cell
lines as described elsewhere (19). Two .mu.g of total RNA were used
for first strand synthesis with random hexamer primers. RT-PCR was
performed with primers specific to the common region (SEQ ID NO:11
and SEQ ID NO:18); the hSef-a (SEQ ID NO:16 and SEQ ID NO:17); the
hSef-b (SEQ ID NO:2 and SEQ ID NO:17); the hSef-c (SEQ ID NO:20 and
SEQ ID NO:19); and the GAPDH transcript (SEQ ID NO:12 and SEQ ID
NO:13). Amplification was performed in a solution of 1 .mu.M of
each oligonucleotide primer, 0.2 mM of each dNTPs, 50 mM KCl, 2 mM
MgCl.sub.2, 1 mM .beta.-mercoptoethanol, 25 mM TAPS pH 9.3 and 0.02
units of Super-Therm polymerase in a total volume of 25 .mu.l.
After pre-denaturation at 95.degree. C. for 5 min, the reaction
mixture was incubated as follows: 30 sec at 94.degree. C., 30 sec
at 65.degree. C., and 2 min at 72.degree. C. for 25 (GAPDH), 35
(hSef-a and hSef-b) or 40 (hSef-c) cycles. 5 .mu.l of each reaction
were analyzed by gel electrophoresis on 1.8% agarose gels in TAE
buffer (40 mM Tris-acetate, 1 mM EDTA) and stained with ethidium
bromide. The PCR products of the amplification with hSef-c specific
primers were separated by electrophoresis on 3% Nusieve-agarose
gels (3% Nusieve GTC agarose, 1% Seakem LE agarose in TBE buffer)
in TBE buffer (45 mM Tris-Borate, 1 mM EDTA).
[0217] Cell Cultures--HEK 293 and NIH/3T3 cells were grown in
Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal
bovine serum or newborn calf serum, respectively.
[0218] Transient transfections of HEK 293 cells--Transient
transfections of HEK 293 cells were performed using Lipofectamine
Plus in Opti-MEM (Invitrogen). For co-immunoprecipitation (CO-IP)
assays the cells were transiently transfected with hSef-a or hSef-b
in the presence or absence of FGFR1. Briefly, cells were cultured
in 6-cm dishes and were transfected with 3 .mu.g of each FGFR1 and
hSef-a plasmids (for hSef-a/FGFR1 CO-IP) or cells (in 10-cm dishes)
were transfected with 4 .mu.g of FGFR1 and 12 .mu.g of hSef-b
plasmids (for hSef-b/FGFR1 CO-IP).
[0219] Stable transfections in NIH/3T3 cells--Stable transfections
were performed using calcium-phosphate, essentially as described in
Ron, D. et al., 1988 (27). Tet-off NIH3T3 cells [S2-6 cells, a gift
from Dr. David. G. Schatz (28)] were cultured in
histidine-deficient DMEM containing 0.5 mM L-histidinol, serum, and
1 .mu.g/ml tetracycline (tet). HSef-b Tet-off NIH/3T3 cell lines
were established by co-transfection of the S2-6 cells with pTet
splice-hSef-b or the same vector without the insert (i.e., an empty
vector) and pTK-Hyg (Clontech) followed by selection in complete
medium plus 150 .mu.g/ml hygromycin. Colonies of resistant cells
were isolated 3 weeks post transfection.
[0220] Cell Growth and Apoptosis Assays--[.sup.3H]-thymidine
incorporation assay was done in 96-well microtiter plates as
described elsewhere (24, 26). Confluent cultures were growth
arrested in 0.3% serum for 24 hours, and when indicated, tet was
removed 24 hours prior to serum (10%) or growth factors
stimulation. For apoptosis studies, the control cells (S2-6) or
S2-6/hSef-b cells were grown for 48 hours in the presence or
absence of tet. The level of apoptosis was detected using the In
Situ Cell Death detection kit (TUNEL staining, Roche Molecular
Biochemicals) followed by a confocal microscopy examination.
[0221] In vitro translation of the hsef-b construct
(pcDNA3.1/Hygro-hSef-b)--In vitro translation of hSef-b was
performed using TnT Quick Coupled Transcription/Translation System
in the presence of [.sup.35S]-methionine according to
manufacturer's instructions (Promega). Translation products were
analyzed by SDS-PAGE and visualized using Phospho-imaging.
[0222] hSef antibodies--Polyclonal antibodies against hSef were
generated by injecting rabbits with a polypeptide containing the
last 402 residues of hSef fused to the amino-terminal portion of
Bactriophage a T7 .theta.10 protein as described in Studier, F W et
al., 1990 (29).
[0223] CO-IP and immunoblotting--were performed essentially as
described elsewhere (30). Briefly, for CO-IP, cells were lysed 24
hours post transfection in HTNG buffer (20 mM HEPES, pH 7.4, 150 mM
NaCl, 10% glycerol, 1% Triton X-100, 1 mM EGTA, 1 mM NaVO.sub.4 and
protease inhibitors). After incubation with antibody,
immunocomplexes were captured on Protein G Dynabeads (Dynal), and
washed with HTNG buffer. Following SDS-PAGE and immunoblotting,
bound antibodies were visualized by chemiluminescence.
[0224] Immunofluorescence analysis--Transfected HEK 293 cells were
fixed 48 hours post transfection with 4% paraformaldehyde, and
incubated in PBS containing 1% BSA, 0.1% saponin and were subjected
to immunostaining using the anti-myc (.alpha.-myc) antibody
(anti-myc epitope, 9E 10, Santa Cruz, Santa Cruz, Calif.) or the
anti-human Sef antibody (.alpha.-hSef). Nuclear staining was done
using 10 .mu.M DRAQ5 (Biostatus limited, Shepshed, Leicestershire,
UK). Examination of the immunofluorescent staining was performed
using the MRC-1024 laser confocal microscope (BioRad, Hercules,
Calif.).
[0225] Antibodies used in Western Blot and immunoprecipitation
analysis--Commercial antibodies were obtained from various
suppliers. The anti-myc epitope (9E10), p38, MEK, Akt, CDK4 and
FGFR1 (H-76) rabbit polyclonal antibodies were from Santa Cruz; the
phospho- p44/42 MAP kinase [Thr202/Tyr204], E10 mouse monoclonal
antibodies (NEB), Phospho-Akt [Ser473], phospho-p38, peroxidase
conjugated-goat anti-rabbit or anti-mouse IgG were from Sigma; the
cyclin D1 and phospho-MEK were from Cell Signaling (Arundel,
Australia); the FITC conjugated-Goat anti-rabbit IgG was from ICN;
the Rhodamine-RedTM-x-conjugated Affinipure goat anti-mouse IgG was
from Jackson Immunoresearch (West Grove, Pa., USA). The ERK-2
rabbit polyclonal antibodies was a gift from Dr. Y. Granot, Ben
Gurion University, Israel.
Example 1
Cloning of the Human Sef-b Isoform
[0226] Experimental Results
[0227] Database search revealed the presence of additional human
Sef isoforms--A database search with the zfSef sequence revealed an
expressed sequence tag (EST clone AL133097) containing the entire
3'-UTR of hSef and most of its coding region except for the first
170 residues. The remainder of the coding region was obtained by
searching the human genome database for upstream exons of hSef and
based on homology with bovine Sef (EST clone BE750478). A cDNA
fragment encoding the entire open reading frame (ORF) of hSef was
amplified from primary human fibroblast or human fetal brain RNA
(FIG. 1a and data not shown). Human Sef has been mapped to a single
locus on chromosome 3p14.3 (data not shown). Further database
searches with the amino-terminal sequence of hSef revealed an EST
clone from human testes that was 577 nucleotides long and contained
an ORF of 122 residues. This EST clone differed from the original
hSef in its amino-terminal and the upstream 5'-UTR sequences. Since
the human genome contains a single Sef locus, these findings
suggest the existence of alternatively spliced Sef isoforms.
[0228] Cloning of the human Sef-b isoform--To examine the
possibility of additional hSef isoforms, an RT-PCR analysis was
performed as follows: first strand was synthesized using a
complementary to the 3' UTR of hSef (SEQ ID NO:1), Amplification
was performed with primers set forth by SEQ ID NOs:3 and 2. A
single product of 2214 nucleotides was obtained (SEQ ID NO:4),
confirming the existence of alternate isoforms of hSef (designated
hSef-a and hSef-b for the brain and testes isoforms,
respectively).
[0229] Identification of the hSef-b using RACE analysis--The
present inventor also identified the hSef-b common and unique
sequences using the RACE protocol on human keratinocytes RNA with
three consecutive primers designed according to the common region
(e.g., SEQ ID NO:17). The experimentally sequence obtained using
the RACE protocol is provided in SEQ ID NO:22.
[0230] Human Sef-b isoform contains alternative N-terminal amino
acid residues--As is schematically illustrated in FIG. 1, while the
human Sef-a isoforms contains an ORF of 739 residues (SEQ ID NO:5),
the human Sef-b contains an ORF of 707 amino acid residues (SEQ ID
NO:6), of them the last 697 residues (i.e., amino acids 11-707 of
SEQ ID NO:6) are identical in both isoforms. These results
demonstrate the presence of alternative splicing in the human Sef
gene resulting in the substitution of the first 42 amino acid
residues of hSef-a ORF with 10 new residues of the hSef-b ORF.
[0231] Human Sef-b isoform lacks a secretion signal--Similar to
hSef-a, the new isoform contains 8 potential N-linked glycosylation
sites, a potential transmembrane spanning domain and tyrosine
phosphorylation site, immunoglobulin and IL-17 receptor like
domains (FIG. 1). Unlike hSef-a which contains a signal for
secretion [amino acid residues 1-34 as set forth by SEQ ID NO:5;
FIG. 1, marked by a star (*) and the sequence which appears left to
the arrow], the hSef-b isoform lacks such a signal (FIG. 1),
suggesting that it is not a secreted or trans-membrane protein.
[0232] Human Sef-b isoforms contains a putative CUG translation
initiation codon Interestingly, the unique hSef-b region exhibits a
CUG initiation codon. The next putative initiation codon (AUG) is
located within the region that is identical in both isoforms. Thus,
while translation from the CUG codon is expected to result in a
protein of 707 amino acids with a predicted molecular weight of 78
kDa, translation from the AUG codon is expected to result in a
protein of 595 residues and a predicted molecular weight of 65
kDa.
[0233] The hSef-b isoform uses the CUG translation initiation codon
in vitro and in HEK 293 cell cultures--To characterize the hSef-b
product and elucidate whether the alternative initiation codon in
hSef-b can serve as a translation start site, a cDNA fragment
encoding the entire ORF of hSef-b (SEQ ID NO:4) was subcloned into
the either pcDNA3.1/Hygro or in pcDNA3.1/myc-His(+)B eukaryotic
expression vector (Invitrogen) which contains the myc epitope-tag
at the carboxyl terminus of the recombinant hSef-b coding sequence
allowing the detection of the translation product with the a-myc
antibody. As is shown in FIG. 2a, expression of the
pcDNA3.1/myc-His-hSef-b DNA construct in HEK 293 cells revealed a
single protein product with a molecular weight of about 80 kDa.
Similarly, when the hSef-b cDNA was cloned into the pcDNA3.1/Hygro
vector (Invitrogen) and was subjected to an in vitro
transcription-translation in the presence of [.sup.35S]-methionine,
a major product with a similar molecular weight (.about.80 kDa) was
obtained (FIG. 2b). These findings strongly suggest that the CUG
codon functions as a major translation start site in the hSef-b
isoform.
[0234] Human Sef-b is a putative intracellular protein--As is
mentioned hereinabove, and depicted in FIG. 1, both hSef isoforms
have 8 potential N-linked glycosylation sites. Thus, although
hSef-a has a predicted size of 83 kDa, when the coding sequence of
hSef-a was expressed in HEK 293 cells, a broad band with an average
molecular weight of 120 kDa was observed (FIG. 2a), suggesting
massive post-translational glycosylations. On the other hand, the
similarity between the apparent (80 kDa, FIG. 2a) and the predicted
(i.e., 78 kDa) molecular weight of hSef-b suggests that the hSef-b
isoform does not undergo any significant post-translational
modifications. To test the hypothesis that hSef-b, unlike hSef-a,
is not subjected to post-translational glycosylations, transfected
HEK 293 cells were treated with tunicamycin, an inhibitor of
N-linked glycosylation, and the molecular weight of the recombinant
proteins was examined on an SDS-PAGE. While tunicamycin treatment
resulted in a reduced molecular weight of the hSef-a isoform, such
a treatment had no effect on the molecular weight of the hSef-b
product (data not shown).
[0235] Altogether, these results indicate that hSef-a, but not
hSef-b, is a glycoprotein synthesized in the classical secretory
pathway, and further suggest that the hSef-b product is an
intracellular protein.
[0236] Cellular localization of the human Sef isoforms--To further
test the possibility that hSef-b is an intracellular protein,
transfected HEK 293 cells expressing each of the human Sef isoforms
were subjected to immunofluorescence analysis. Detection was
performed using antibodies directed against the myc epitope-tag
fused to the hSef products or antibodies directed against the
carboxyl-terminus of hSef proteins. As shown in FIGS. 3a-d, while
hSef-a was localized to the cell surface (in agreement with prior
art findings Tsang, M. et al., 2002) the hSef-b protein was
detected in the cytosol of the transfected cell. These findings
demonstrate that the hSef-b product is a cytosolic protein.
[0237] Altogether, these results demonstrate that the hSef gene
undergoes alternative splicing which result in at least two
distinct hSef isoforms (hSef-a and b). These results further show
that while hSef-a is a heavily glycosylated, membrane protein, the
hSef-b isoform apparently lacks any post-translational
glycosylation modifications and is localized to the cytosol.
Example 2
The Expression of Human Sef Isoforms is Differentially
Regulated
[0238] To further understand the role of the newly identified
hSef-b isoform, the expression pattern and function of the hSef
isoforms were determined, as follows.
[0239] Experimental Results
[0240] Tissue type specific expression of human Sef isoforms--The
pattern of expression of hSef isoforms in a variety of human
tissues and cell lines was examined by RT-PCR. Primers were
designed to amplify a region common to both hSef transcripts or to
specifically amplify each transcript. All 16 samples examined were
positive for Sef transcripts when amplified with the primers from
the common region of Sef isoforms (FIG. 4a). As is shown in FIG.
4b, hSef-a transcript was differentially expressed in 15 samples;
HSef-a transcript was highly expressed in both fetal and adult
brain, pituitary, tonsils, spleen, adenoids, fetal kidney, liver,
testes and ovary, and moderate levels were detected in primary
aortic endothelial cells, human umbilical vein endothelial cells
(HUVEC) and adrenal medulla. As is further shown in FIG. 4b, low
levels of hSef-a were observed in adrenal cortex, barely detected
in placenta and completely absent in thyroid. In contrast, as is
shown in FIG. 4c, hSef-b transcript was highly expressed in thyroid
and testes; moderately expressed in pituitary, fetal brain and
HUVEC cells; remaining tissues were either negative or expressed
barely detectable levels of the hSef-b transcript. These findings
demonstrate a unique expression pattern of hSef isoforms in a
variety of tissues and suggest that the expression of the human Sef
isoforms is regulated at the level of splicing or mRNA
stability.
Example 3
Human Sef-B Isoform Inhibits Proliferation of OF NIH/3 T3 Cells and
Interferes with Human HEK 293 Cell Growth
[0241] The different biochemical properties and subcellular
localization of the two hSef isoforms raised the question whether
hSef-b can inhibit FGF biological activity similar to hSef-a.
NIH/3T3 cells were chosen to study the effect of hSef-b on
biological responses to FGFs since they proliferate in response to
various members of the FGF family, and have been extensively
utilized as a model to study oncogenesis, regulation of cell
proliferation and growth factor-mediated signaling. In addition,
preliminary RT-PCR analyses revealed that NIH/3T3 cells express the
mouse-Sef gene (data not shown). To study the effect of hSef-b on
NIH/3T3 proliferation, cells were transfected with an expression
vector containing the hSef-b coding sequence and the effect of
hSef-b expression on colony number and proliferation was studied,
as follows.
[0242] Experimental Results
[0243] Human Sef-b isoform reduces the number of NIH/3T3
colonies--The general effect of hSef-b on the growth of NIH/3T3
cells was studied as follows. Cells were stably transfected with
either the pcDNA/hSef-b or an empty vector (i.e., a pcDNA without
the hSef-b insert) and one day following transfection the cells
were diluted (1:25) and were further cultured for 2-3 weeks in the
presence of hygromycin B (marker selection), following which
resistant colonies were counted. As is shown in Table 1,
hereinbelow, a significant decrease (75%) in the number of colonies
was observed in cells transfected with the hSef-b expression vector
as compared with cells transfected with the empty vector.
TABLE-US-00001 TABLE 1 Number of colonies in cell stably
transfected with hSef-b vector No. of colonies Ratio (%) Empty
vector 110 100 hSef-b 28 25.9 Table 1: NIH 3T3 cells were stably
transfected with either an expression vector (pCDNA3.1) containing
the hSef-b coding sequence (SEQ ID NO: 4) or with the pCDNA3.1
vector alone (empty vector) and 2-3 weeks following transfection in
the presence of the hygromycin B selection the number of colonies
(five plates for each vector) was counted. Results represent the
average of three independent experiments.
[0244] These results clearly demonstrate that similarly to hSef-a,
hSef-b isoform inhibits NIH/3T3 cell growth.
[0245] Establishment of tet-off hSef-b NIH 3T3 cells lines--To
understand the mechanisms leading to the inhibitory effect of
hSef-b on the number of colonies of NIH 3T3 cells and to study the
effect of hSef-b on FGF mediated signaling, NIH 3T3 stable cell
lines in which the expression of hSef-b is regulated by
tetracycline (tet) were established. S2 cells (NIH 3T3) were
co-transfected with the pTet splice-hSef-b or an empty vector
(i.e., the pTet splice alone, control cells) and the pTK-Hyg vector
and were cultured for three weeks in the presence of hygromycin.
Clones that did not express detectable levels of hSef-b in the
presence of tetracycline were chosen for further analysis. Maximal
level of hSef-b protein was obtained 16 hours following removal of
tetracycline (FIG. 5, and data not shown).
[0246] Expression of hsef-b in NIH/3T3 cells does not affect the
level of apoptosis--The inhibitory effect of hSef-b on colony
formation could have resulted from either induction of apoptosis or
inhibition of cell growth. The effect of hSef-b on apoptosis was
tested using the TUNEL staining. Stable transfectants of hSef-b NIH
3T3 cells were grown for 48 hours in the presence or absence of
tetracycline, or in the absence of tetracycline and serum,
following which the cells were washed and fixed and were subjected
to a TUNEL assay. As is shown in FIGS. 6a-c, while apoptotic cells
were readily detected in NIH 3T3 cells grown in the absence of
tetracycline and serum (FIG. 6c), no significant level of apoptosis
was observed in NIH 3T3 grown in the presence (i.e., when hSef-b
expression is downregulated) or absence (i.e., when hSef-b
expression is upregulated) of tetracycline (FIGS. 6a and 6b,
respectively).
[0247] Thus, these results demonstrate that over-expression of
hSef-b in cells doesn't affect apoptotic processes in the
cells.
[0248] Over-expression of human Sef-b affects the growth of human
HEK 293 cells--When HEK 293 cells were transiently transfected with
the hSef-b expression vector the morphology of the cells was
changed (i.e., more round cells) and the cells came easily off the
plate (data not shown). These results suggest that hSef-b affects
the normal growth of human cells and likely causes cell death.
[0249] Human Sef-b inhibits NIH 3T3 growth via inhibition of the
FGF2 mitogenic activity--To test the possibility that expression of
hSef-b involves in FGF2 mitogenic activity, [.sup.3H]-thymidine
incorporation assays were employed. Confluent cultures of control
or hsef-b-expressing cells were serum starved (for 24) and were
grown in the presence or absence of tetracycline, following which
the level of [.sup.3H]-thymidine incorporation was measured in the
presence of increasing concentrations of FGF2. As is shown in FIGS.
7a-b, while in control cells [.sup.3H]-thymidine incorporation
increased along with the increase of FGF2, in hSef-b-expressing
cells, at 0.7 ng/ml FGF2, [.sup.3H]-thymidine incorporation was
reduced. These results demonstrate that over-expression of hSef-b
strongly inhibits the mitogenic activity of FGF2.
[0250] Altogether, these findings indicate that hSef-b acts by
restricting cell division and not by inducing apoptosis in NIH/3T3
cells.
Example 4
Human Sef-B Prevents Activation of ERK1/2 MAP-Kinases
[0251] To further understand the mechanisms leading to
hSef-b-mediated inhibition of cell growth the present inventor has
studies the level of Cyclin-D1 which regulates S-phase entry (31),
as well as the level of Erk1/2 MAP-kinases, pkB/Akt and p38
MAP-kinase, which are known to regulate cyclin D1 levels by
transcriptional and post-translational mechanisms (31, 32). Erk1/2
MAP-kinases enhance Cyclin D1 expression and regulate the assembly
of cyclin-CDK complex, whereas pkB/Akt regulates the turnover of
cyclin D1 protein (31, 32). The p38 MAP-kinase can inhibit Cyclin
D1 expression in a cell type dependent manner. p38 MAP-kinase has
been generally associated with cellular response to stress, but
several reports suggest its involvement in cellular responses to
growth factors including FGF2 (22, 23).
[0252] Experimental Results
[0253] The hsef-b isoform reduces the level of cyclin
D1--Sef-inducible cell lines were utilized to explore the mechanism
underlying hSef-b inhibition of cell division. Cyclin D1 protein
levels were evaluated at different time intervals post FGF2
growth-factor stimulation. As is shown in FIG. 8, while 20 hours
following growth factor stimulation the cyclin D1 protein was
readily observed in cells cultured in the presence of tetracycline,
hSef-b-expressing cells failed to express cyclin D1. Since the
levels of cyclin dependent kinase 4 (CDK4) do not fluctuate during
the cell cycle (31), the level of CDK4 was examined as a probe for
protein levels in each time point. CDK4 levels were similar in all
time points in cultures grown in the presence or absence of
tetracycline (FIG. 8). In addition, the levels of cyclin D1
remained unchanged in the control cells grown with or without
tetracycline (data not shown).
[0254] Human Sef-b isoform prevents the activation of Erk1/2
MAP-kinases--Stimulation over time of control cells and hSef-b
expressing cells revealed that hSef-b inhibited the activation of
Erk1/2 MAP-kinases (phosphorylated Erk1/2) whereas total Erk1/2
levels remained unaltered (Compare P-Erk1/2 (activated) and Erk1/2
in FIGS. 9a and b). On the other hand, HSef-b had no effect on FGF2
induced activation of pkB/Akt or p38 MAP-kinase (FIG. 9a).
[0255] Expression of hsef-b does not affect MAP-kinase kinase level
and state of activation--To further localize the site of hSef-b
action, its effect on the activation of the dual specificity
MAP-kinase kinase (MEK1/2), which phosphorylate Erk1/2 was examined
in response to growth factor stimulation. As is shown in FIG. 9a,
hSef-b had no effect on MEK1/2 activation in FGF2 stimulated cells,
suggesting that the MAPK signaling pathway is blocked at the level
or downstream of MEK.
[0256] The hsef-b protein associates with FGFR1--Prior studies
utilizing co-immunoprecipitation assays demonstrated the
association of the cell surface Sef isoform with several members of
the FGFR family. Moreover, the site of interaction between the cell
surface Sef and FGFR was mapped to the intracellular domain (8, 10,
13). Since as is shown in Example 1 hereinabove, the intracellular
domain of hSef-a is shared in common with the hSef-b isoform, the
ability of hSef-b to form a complex with FGFR1 was tested. To this
end, HEK293 cells were transiently transfected with myc-tagged Sef
constructs in the presence or absence of FGFR1. As shown in FIGS.
10a-b, FGFR1 co-immunoprecipitated with hSef-a in the absence of
ligand stimulation, in agreement with published data (8, 10, 13).
Human Sef-b, notwithstanding its lower expression levels compared
to hSef-a, efficiently associated with FGFR1 but not with EGF
receptor (FIGS. 10a-b and data not shown). These results lend
further support to the importance of the C-terminal domain of Sef
for the association with FGFRs.
Example 5
HSef-B Inhibits the Mitogenic Activity of FGF1, FGF2, FGF4, and
PDGF
[0257] The subcellular localization of hSef-b may extend the
repertoire of receptor tyrosine kinases (RTKs) that it can inhibit.
To explore this hypothesis, the effect of hSef-b on mitogenic
activity of additional members of the FGF family, as well as a
subset of other RTK ligands, and serum was examined, as
follows.
[0258] Experimental Results
[0259] A dose response curve was performed for each ligand, and
representative results are shown in FIGS. 11a-b. In addition to
FGF2, hSef-b inhibited the mitogenic activity of FGF1 and FGF4 (80%
inhibition of FGF2, and 60% inhibition of FGF1 or FGF4) as well as
the activity of platelet derived growth factor (PDGF) (40, 57 and
68% inhibition at 2.5, 5 and 10 ng/ml ligand, respectively). These
results are in contrast the lack of effect of Sef-a on PDGF
signaling (10). Inhibition of PDGF was accompanied with reduction
in the activation of Erk1/2 MAPK (FIG. 12). By contrast, hSef-b had
little or no effect on the activity of serum, insulin or EGF (FIG.
11b). The mitogenic activity of serum and each of the other growth
factors was similar in control cultures grown in the presence or
absence of tetracycline (FIG. 11a).
Example 6
Identification of Additional Human Sef Splice Forms: HSef-C and
HSef-D
[0260] Experimental Results
[0261] Identification of additional alternative spliced forms of
hSef--Using the RACE protocol the present inventor has identified
two additional human Sef isoforms from normal human ovary RNA.
FIGS. 13a and 14a depict the nucleic acid sequences of hSef-c and
hSef-d RACE products, respectively. The predicted amino acid
sequences are shown in FIGS. 13b and 14b, for hSef-c and hSef-d,
respectively. First strand was using the primer set forth by SEQ ID
NO:1, and amplification was performed using the primers set forth
by SEQ ID NOs:19 and 3 (for hSef-c) or SEQ ID NOs:21 and 3 (for
hSef-d), RT-PCR fragments of approximately 2.2 kb each were
identified (data not shown), indicating that the hSef-c and hSef-d
are alternative splice forms of the hSef gene. These results
suggest the identification of the entire coding region of each
isoform. Both isoforms exhibit sequences which are common with the
other hSef isoforms (i.e., hSef-a and hSef-b), these include amino
acids 50-77 in SEQ ID NO:15 (hSef-c) and amino acids 71-115 in SEQ
ID NO:14 (hSef-d). Noteworthy, that while amino acids 21-98 of SEQ
ID NO:14 were predicted from the experimentally identified RACE
product, the rest of the sequence set forth in SEQ ID NO:14 was
predicted using the EST clone (GenBank Accession No. BG149830).
[0262] Prediction of open reading frame within the new hSef
isoforms--In the coding sequence of human Sef-c isoform there are
three potential initiation codons (methionine residues, labeled
with a green M in FIG. 13b), and further experiments (e.g., using
Edman degradation or Mass Spectrometry) are expected to reveal the
active translation initiator. On the other hand, in hSef-d, the
predicted initiation codon is the Methionine residue at position 57
of SEQ ID NO:14.
[0263] Differential expression of hSef-c in breast and
ovary--RT-PCR analysis using primers specific to hSef-c (SEQ ID
NOs:19 and 20) revealed differential expression of this isoform;
hSef-c is highly expressed in breast and ovary tissues, moderately
expressed in brain and to a much lesser extent in fetal kidney
(data not shown).
[0264] Analysis and Discussion The results presented in Examples
1-6, hereinabove, indicate that different hSef isoforms are
generated via an alternative splicing mechanism. One isoform,
hSef-a, is similar to the previously reported Sef from zebrafish
and mammals (7-9, 13). This isoform is thought to encode a type I
transmembrane protein, and immunofluorescence staining confirmed
that hSef-a product is located at the cell surface. On the other
hand, in the novel isoform, hSef-b, the leader sequence and the
next 8 residues of hSef-a were replaced with 10 different residues.
This isoform lacks a signal for secretion and immunofluorescence
staining revealed that it is a cytosolic protein. Furthermore, the
hSef-b product does not undergo significant post-translational
modifications, a property that is typical for proteins that are
translated in the cytosolic compartment. Collectively these results
demonstrate that alternative splicing differentially influences the
subcellular localization of hSef isoforms.
[0265] Besides lacking a signal for secretion, the alternate
sequence contained a CUG initiation codon instead of the
conventional AUG initiation codon. Initiation from this CUG codon
is consistent with the apparent molecular weight of both the in
vitro and in vivo expressed hSef-b. The utilization of CUG as a
translation start site may be responsible for the observed
differences in the expression levels of hSef-a and hSef-b products,
as non-AUG codons direct less efficient translation initiation (34,
35).
[0266] The hSef-b isoform exhibits a restricted pattern of
expression compared to hSef-a. It is highly expressed in testes and
thyroid and to a much lesser extent in tissues of neuronal origin
and primary endothelial cells whereas hSef-a transcript is
expressed in all the tissues and primary cells that were examined
except for the thyroid. Interestingly, the expression profile of
hSef-a parallels that of FGFRs (19, 20, 36-38) suggesting that this
isoform regulates a wide array of biological processes where FGFs
are implicated. The high levels of hSef-b in thyroid and testes
could imply that this isoform regulates unique biological processes
and may be more specific to cells of epithelial origin. With
respect to FGFs, it may control signaling by specific receptor
isoforms. Therefore, an important avenue of future research would
be to determine how each Sef isoform affects signaling by the
distinct FGFRs.
[0267] Human Sef-b inhibited mitogenic response of NIH/3T3 cells to
several members of the FGF family, but not to serum, insulin or
EGF. Unlike the cell surface Sef (10), hSef-b inhibited
PDGF-induced mitogenic response suggesting that intracellular
machinery, common to signaling by FGF and PDGF, is affected.
Consistent with this is the finding that hSef-b inhibited the
Ras/MAPK pathway and reduced cyclin D1 levels. However, hSef-b does
not globally affect RTK-induced signaling pathways since it had no
effect on FGF induction of the PI 3-kinase or the p38 MAPK pathway,
which is consistent with hSef-b action downstream of Ras. Lack of
an effect on the PI 3-kinase pathway also correlates with the
finding that hSef-b inhibited cell growth but did not lead to an
increase in apoptosis. The inhibition of the MAPK pathway and
maintenance of PI 3-kinase pathway may allow cells expressing
hSef-b to cease proliferation but remain viable upon growth factor
stimulation.
[0268] Altogether these results restrict hSef-b activity to a
narrow window at the level of, or down stream from MEK. Similar to
the hSef-a isoform [(8, 10, 13), and present data], the hSef-b
isoform can associate with FGFR1 in co-immunoprecipitation assays.
Since, unlike hSef-a, the hSef-b isoform is cytosolic, its
association with the receptor could function as a mean to bring
hSef-b in the vicinity of the components of the Ras/MAPK pathway.
Although both isoforms interact with FGFR1, the outcome of this
association is not identical because the cell surface Sef isoform
inhibits multiple FGF-signaling pathways [(10), and data not
shown]. As the entire hSef-b isoform is located inside the cells,
its folding must be quite different from that of the hSef-a
isoform, and is likely to influence its mode of action. For
example, the amino-terminal domain of hSef-b, which also contains
the unique hSef-b residues, can interact with proteins in the
signaling cascade whereas in hSef-a, this domain is extracellular
and is not required for inhibitory activity (8, 10, 13).
Alternatively, it could function as an autoregulatory domain that
prevents hSef-b from interacting with certain proteins in the
signaling cascade. Studies are in progress to address these
questions.
Example 7
Human Sef-B Induces Efficient Colony Suppression and Inhibits
Growth of Breast Cancer Cell Lines
[0269] Materials and Experimental Methods
[0270] Cell Culture, transfection methods and colony suppression
assay--Human cell lines MDA-MB-435, HeLa, and human embryonic
kidney, HEK 293, were maintained in Dulbecco's modified Eagle's
medium (DMEM) supplemented with 10% fetal bovine serum (FCS). For
transfection, cells from sub-confluent cultures were plated at a
density of 2.times.10.sup.6 cells per 60 mm plate, and 24 hours
later, were transfected with either the hSef-a [pcDNA3.1/hSef-a
(SEQ ID NO:10), containing the hygromycin selection marker], the
hSef-b [pcDNA3.1/myc-His/hSef-b (SEQ ID NO:4), containing the
neomycin selection marker] or the hSef-c [pcDNA3.1/hSef-c (SEQ ID
NO:8)] expression vectors (5 .mu.g DNA per plate). An empty
pCDNA3.1 vector was used as control. Transfection was performed
with DreamFect reagent according to the manufacturer's instructions
(OZ Biosciences). Six to eight hours post transfection, the medium
was replaced with fresh DMEM containing 10% FCS. The following day,
cultures were trypsinized and plated at various dilutions (e.g.,
1:5 and 1:10). Selection was carried out with complete medium
containing 1 mg/ml G418 or 150 .mu.g/ml hygromycin (depending on
the plasmid used). Colonies of resistant cells were counted at the
end of the selection process 1-2 weeks post transfection.
[0271] Experimental Results
[0272] Overexpression (ectopic expression) of hSef-a, hSef-b or
hSef-c results in suppression of colony formation and reduced cell
growth of MDA-MB 435 breast cancer cells--To ascertain the
biological effect of hSef expression in human cancer cells, a
colony suppression assay was employed. The breast cancer cell line
MDA-MB-435, extensively used for studying breast cancer biology
(Sellappan, S., Grijalva, R., Zhou, X., Yang, W., Eli, M. B.,
Mills, G. B. and Yu, D. Lineage infidelity of MDA-MB-435 cells:
expression of melanocyte proteins in a breast cancer cell line,
Cancer Res., 64: 3479-3485, 2004), was transfected with either
hSef-a, hSef-b or hSef-c expression vectors and colonies were
counted 1-2 weeks following marker selection. Cells transfected
with hSef-a, hSef-b or hSef-c expression vector formed about 94-95%
less colonies as compared with cells transfected with control empty
vector (Table 2, hereinbelow). It is noteworthy, that while the
majority (over 95%) of resistant colonies transfected with the
control empty vector were dense, the colonies formed following
transfection with the hSef-b, hSef-a or hSef-c were very sparse,
small, made of few cells, grew extremely slowly, and the majority
did not survive trypsinization and plating. TABLE-US-00002 TABLE 2
Number of colonies in cell stably transfected with hSef-a, hSef-b,
hSef-c or empty vector Vector No. of colonies Ratio (%) Empty
vector 250 100 hSef-a 15 6 hSef-b 12 5 hSef-c 12 5 Table 2: MDA-MB
435 cells were stably transfected with expression vector bearing
hSef-a (pCDNA/hSef-a), hSef-b (pCDNA/hSef-b), hSef-c
(pCDNA3.1/hSef-c) or an empty vector (pCDNA). After one day, cells
were diluted and marker-selected for 1-2 weeks. Resistant clones
were counted at the end of the selection process (3 plates for each
vector). The results are representative of 3 different experiments,
and show the average number of colonies/plate.
[0273] Altogether, these results clearly demonstrate that
overexpression of hSef-a, hSef-b or hSef-c results in a significant
inhibition of cancerous colony formation and cancerous cell
growth.
Example 8
Downregulation of Sef Expression Correlates with Increased
Malignancy of Solid Tumors
[0274] As described in Example 2, hereinabove, hSef is highly
expressed in the epithelial cells of normal breast, prostate and
the thyroid glands as well as the ovarian surface. To further
substantiate the role of hSef in the initiation and/or progression
of solid tumors, the present inventor has further investigated the
expression of Sef in normal epithelial tissues and cancer derived
from these tissues.
[0275] Materials and Experimental Methods
[0276] Enzymes, Reagents, Chemicals, and expression
vectors--Restriction enzymes were from NEB, Pharmacia and Roche.
Blocking reagent, Digoxigenin (DIG)-RNA Labeling Kit,
5-Bromo-4-chloro-3-indolyl-phosphate, 4-toluidine salt, Nitroblue
tetrazolium chloride, maleic acid, T7 RNA Polymerase, Proteinase K,
Yeast tRNA and Anti-digoxigenin [Fab] conjugated to alkaline
phosphatase were from Roche. M-MLV Reverse Transcriptase and random
hexamer primers were from GIBCO BRL. Mounting solution was from
Southern Biotech, BSA from ICN, and all other chemicals were from
Sigma. Expression plasmids containing the hSef-a or hSef-b coding
region were generated as described in the "General Marterials and
Experimental Methods" of the Examples section, hereinabove. The
different hSef cDNA isoforms (hSef-a or hSef-b) were cloned into
pcDNA3.1, or pcDNA3.1/myc-His expression vectors (Invitrogen)
containing the hygromycin or neomycin selection marker,
respectively.
[0277] RNA extraction and RT-PCR--For detection of hSef transcripts
in normal breast tissues, total RNA was extracted from human breast
tissues, as described (Eisemann, A., et al., Oncogene, 6:
1195-1202, 1991; Preger, E., et al., Proc Natl. Acad. Sci. U.S.A,
101: 1229-1234, 2004). Half microgram (0.5 .mu.g) of total RNA was
used for first-strand synthesis with random hexamer primers. The
PCR was performed with a primer common to both hSef isoforms
(5'-TGAAGCTACTGTTGAGCTGCTTCG-3' SEQ ID NO:17) and a primer specific
for each isoform. (hSef-a;
5'-GAGGATCCTGACGGCCATGGCCCCGTGGCTGCAGCT-3' SEQ ID NO:16 or hSef-b;
5'- GCGTGCCAGACAGAGTGCTAGGCAT-3' SEQ ID NO:2). Amplification was
carried out in 25 .mu.l using standard conditions of 1 .mu.M
primers, using Redimix (ABgene), for 32 cycles at 95.degree. C. for
30 seconds, 64.degree. C. for 30 seconds and 72.degree. C. for 1
minute. For detection of hSef RNA in HeLa cells, 1 .mu.g of total
RNA was used for first strand synthesis, and amplification was
carried out with primers common to hSef isoforms as previously
described (Preger et al., PNAS 2004, Supra). GAPDH amplification
was carried out for monitoring RNA quantity and amplification
efficiency.
[0278] Tissue microarrays, tissue sections, and in situ
hybridization--Tissue microarrays containing 1.5 mm cores of normal
and cancer tissues were purchased from Cybrdi, Gaithersburg, Md.
The microarray contained breast cancer specimens from 62 different
cases, 53 ovarian cancer specimens, 33 prostate cancer specimens in
duplicate, or 16 thyroid carcinoma specimens in triplicate.
Morphology of each tissue was confirmed by hematoxylin & Eosin
staining. All samples were pathologically confirmed prior to
hybridization by the manufacturer, and following in-situ
hybridization by two experienced pathologists. Formalin fixed,
paraffin embedded sections of breast and prostate tumors as well as
normal breast, ovary, and thyroid tissues were obtained from the
Departments of Pathology, Rambam Medical Center, (Haifa, Israel),
and the Bnai Zion Medical Center, (Haifa, Israel). Grading of
breast and thyroid cancers was according to the World Health
Organization criteria (for breast: Tavassoli F A, Devilee P. eds
In: World Health Organization classification of tumours. Pathology
and Genetics of Tumors of the breast, and female genital organs.
Lyon: IARC Press; 2003. p.18-19; for thyroid: DeLellis R A, Llowd R
V, Heitz P U, Emg C eds. In: World Health Organization
classification of tumours. Pathology and genetics of tumors of
endocrine organs. Lyon:IARC press; 2004. p. 64); ovarian carcinomas
were graded according to the International Federation of Gynecology
and Obstetrics (FIGO) grading system, and prostate cancer grading
was according the Gleason grading system (for prostate: Maygarden,
S. J. and Pruthi, R. Gleason grading and volume estimation in
prostate needle biopsy specimens: evolving issues, Am. J. Clin.
Pathol., 123 Suppl:S58-66.: S58-S66, 2005; for ovarian: Kosary, C.
L. FIGO stage, histology, histologic grade, age and race as
prognostic factors in determining survival for cancers of the
female gynecological system: an analysis of 1973-87 SEER cases of
cancers of the endometrium, cervix, ovary, vulva, and vagina,
Semin. Surg. Oncol., 10: 31-46, 1994). RNA in-situ hybridization
was carried out as previously described (Sher, I., et al.,
Targeting perlecan in human keratinocytes reveals novel roles for
perlecan in epidermal formation, J. Biol. Chem., 281: 5178-5187,
2005). For probe preparation, a cDNA fragment spanning nucleotides
1606-2208 from the hSef common region (accession # AY489047) and
cloned in both orientations, relative to the T7 RNA polymerase
promoter, into pBluescript II plasmid (Stratagene).
Digoxigenin-labeled (DIG) antisense and sense riboprobes were
synthesized by using T7 RNA polymerase according to the
manufacturer's protocol. Probe preparation, sectioning,
pretreatment of the sections, and hybridization of the probes were
done under strict RNase-free conditions, using reagents supplied by
Roche Applied Science. All reagents were prepared using diethyl
pyrocarbonate-treated distilled water. Sections (5 .mu.m thick)
were incubated overnight at 45.degree. C. in the prehybridization
solution containing 0.5 .mu.g/ml of DIG-labeled RNA probe, for the
breast, prostate and thyroid sections, and 1 .mu.g/ml for the ovary
sections. The detection of the hybridized probes was carried out
using anti-DIG antibodies alkaline phosphatase-conjugated
(antibodies dilution 1/2500) in 4.degree. C. for 16 hours. The
signal was detected using the NBT/BCIP substrates. Where indicated,
sections were counterstained with Mayer's hematoxylin.
Hybridization with the sense probe used as hybridization
specificity control and did not result in detectable signal. Slides
were analyzed with a Nikon eclipse E400 microscope. Staining
intensity was semiquantitatively classified as very strong (typical
for normal epithelium), strong (few tumors with .about.50-75%
staining intensity of normal epithelium), moderate (.about.25-50%
intensity of normal epithelium), weak (<25% of normal
epithelium) and negative (<5% of normal epithelium). Statistical
significance of associations between tumor grade and hSef
expression was determined by Chi square test.
[0279] Experimental Results
[0280] Expression of hSef-a, but not hSef-b, in normal human breast
tissues--To determine whether hSef is expressed in normal mammary
epithelium, and to find out which of the hSef isoforms is expressed
in breast tissues, initial RT-PCR analysis was employed. The
analysis was performed with RNA extracted from different healthy
donors using primer sets that specifically detect the hSef-a or the
hSef-b isoforms. As is shown in FIG. 15a, hSef-a but not hSef-b, is
expressed in normal human breast. In situ analysis with probe
common to the different hSef isoforms revealed in normal human
breast tissue very strong hSef signal in the ductal and lobular
epithelial cells (Ep) and a weaker signal in stromal fibroblasts
(F) and endothelial cells (FIGS. 15b-c). hSef transcripts were not
detected in vascular smooth muscle cells (Vsm), myoepithelial cells
(My) and adipose tissue (Ad) (Data not shown). A sense probe failed
to generate a signal (data not shown) confirming specificity of
hSef transcript detection.
[0281] The expression of hsef is downregulated in invasive breast
cancer--The expression of hSef in 68 carcinoma cases and 2 benign
lesions was surveyed by RNA in situ hybridization. Two of 68 cases
were classified as well-differentiated non-invasive carcinoma
(grade I), and 66/68 cases as invasive carcinoma (6, 43, and 17
grade I, II, and III, respectively). Representative illustrations
and a summary of hSef expression levels in the different cancer
types are shown in FIGS. 15d-i and Table 3, respectively. Ductal
epithelial cells of benign lesions and non-invasive carcinoma
exhibited high hSef expression levels close to the very strong
staining of normal mammary epithelial cells (FIG. 15d and data not
shown). In contrast, striking reduction in hSef expression was
observed in the invasive carcinoma cases: 7/66 tumors expressed
uniformly weak hSef levels (FIG. 15f), 3/66 displayed heterogeneous
expression pattern (FIG. 15e), and 56/66 tumors were negative
(FIGS. 15g-i). The 3 tumors with heterogenous expression, diagnosed
as grade I well differentiated invasive carcinoma, displayed a
mixed morphology with more than 85% solid growth pattern, and less
than 15% ductal architecture. Strong hSef expression was observed
in only a small fraction of the cancerous ducts whereas the rest of
the tumor was negative or expressed low hSef levels (FIG. 15e). The
negative cases were 1/6 grade I, 40/43 grade II, and 15/17 grade
III (see Table 3, hereinbelow). These results, therefore, indicate
a strong association between loss of hSef expression and breast
cancer invasion. TABLE-US-00003 TABLE 3 Summary of hSef expression
in breast carcinomas Expression Level Histological type N Very
Strong Low Negative Non-invasive 2 2 carcinoma (DCIS low grade)
Invasive carcinoma/ 6 5.sup.a 1 grade I grade II 43 3 40 grade III
17 2 15 Number of cases 68 (100%) 2 (3%) 10 (14%) 56 (83%) examined
Table 3 - hSef expression levels in breast carcinomas according to
tumor grade. Expression levels in tumors were compared to those
observed in normal ductal epithelial cells (8 cases). Signal
intensity score was determined as described under the Materials and
Experimental Methods. .sup.adenotes heterogeneous staining observed
in 3 tumor samples diagnosed as grade I well differentiated
invasive carcinoma. In these tumors hSef signal was low in about
75-90% of the tumor cells, and moderate to strong in about 10-25%
tumor cells where ductal architecture was still apparent (see FIGS.
17a-j). Examples for the different staining intensities are shown
in FIGS. 15b-i.
[0282] Down regulation of hSef expression is common to a variety of
human epithelial tumors--To determine whether the profound
reduction in hSef expression during breast cancer invasion is
organ-specific or common to epithelial carcinogenesis in vivo, the
present inventor has expanded the analysis comparing hSef
expression in normal tissues and malignancies of the ovary,
prostate and thyroid gland. Representative expression analysis by
RNA in situ hybridization is illustrated in FIGS. 16a-f (ovary),
17a-f (thyroid) and 18a-f (prostate) and comprehensive results of
hSef expression levels in various cancer types are summarized in
Table 4, hereinbelow.
[0283] As shown in FIGS. 16a-b, hSef transcript levels were high in
ovarian surface epithelium (OSE) and epithelium of the fallopian
tube (FT) (4 cases). This was consistent with detection of hSef-a
expression in normal human ovary using RT-PCR (Preger, E., et al.,
Proc Natl. Acad. Sci. U.S.A, 101: 1229-1234, 2004). For comparison
of hSef expression in epithelial ovarian cancer (EOC), 43 primary
ovarian epithelial tumors and 10 secondary ovarian malignancies
were analyzed. EOC is the sixth most common cancer in women and the
most frequent cancer-related cause of death from gynecologic tumors
(Jemal, A., et al., Cancer statistics, 2006, CA Cancer J. Clin.,
56: 106-130, 2006; Bell, D. A. Origins and molecular pathology of
ovarian cancer, Mod. Pathol., 18 Suppl 2:S19-32.: S19-S32, 2005).
Ninety-five percent of EOC originate from the ovarian surface
epithelium (OSE), where high hSef levels were detected, and
.about.5% of EOC represent metastases from other organ sites (Bell,
D. A., 2005, Supra; Kaku, T., et al., Med. Electron Microsc., 36:
9-17, 2003). Thirty-two primary EOC represented serous carcinomas,
the most common ovarian malignancy (Jemal, A., 2006, Supra; Bell,
D. A. 2005, Supra). The remaining 11 primary tumors were EOC of
lower incidence including mucinous, endometrioid, clear cell and
undifferentiated tumors. The group of primary EOC comprised 12% (
5/43 cases) grade I, 35% ( 15/43) grade II, and 53% ( 23/43) grade
III tumors. Secondary malignancies included metastases from the GI
tract and breast (9 and 1 case, respectively). hSef was clearly
down-regulated in 95% of primary EOCs exhibiting low expression in
17/43 cases and was undetectable in 19/43 cases (FIGS. 16e-f and
Table 4). In the remaining 7/43 cases, moderate hSef expression was
observed in 5 (3 cases of grade II and 2 of grade III) and strong
expression in 2 low grade tumors (FIGS. 16c-d). Among the
metastatic tumors to the ovary, nine out of ten cases were
negative, and 1 case expressed low hSef levels (Table 4). These
findings clearly indicate that hSef expression was also
down-regulated in tumors of the ovary.
[0284] Thyroid carcinoma is the most common malignancy of the
endocrine system, and the majority of tumors originate from the
follicular cells of the thyroid gland (DeLellis R A, Llowd R V,
Heitz P U, Emg C. (ed). World Health Organization classificatin of
tumours. Pathology and genetics of tumors of endocrine organs, IARC
press: Lyon, 2004; Hundahl, S. A., Fleming, I. D., Fremgen, A. M.
and Menck, H. R. A National Cancer Data Base report on 53,856 cases
of thyroid carcinoma treated in the U.S., 1985-1995, Cancer., 83:
2638-2648, 1998). As shown in FIGS. 17a-b, a very strong hSef
signal was observed in the follicular cells of normal thyroid (n=3)
confirming detection of hSef by RT-PCR (Preger, E., 2004, Supra).
Sixteen thyroid malignancies screened for hSef expression included
8 papillary and 8 follicular carcinomas (summarized in Table 4).
These tumor types arise from the follicular cells of the thyroid
gland where hSef transcripts are expressed physiologically.
Papillary carcinoma is a slow growing cancer, accounting for 70-80%
of all thyroid cancers. Follicular carcinoma is generally
considered more aggressive than papillary carcinoma and accounts
for about 15% of thyroid gland tumors (Gimm, O. Thyroid cancer,
Cancer Lett., 163: 143-156, 2001). hSef transcripts were absent in
75% of the tumors (5/8 papillary, 7/8 follicular, FIGS. 17e-f). The
staining intensity in the remaining 4 cases, which were from low
grade tumors, was strong in 3 (2 papillary and 1 follicular
carcinoma) and moderate in the forth case [(papillary carcinoma),
FIGS. 17c-d]. These results demonstrate a marked reduction of hSef
expression in thyroid carcinomas.
[0285] Prostate cancer is the most common visceral cancer and the
second leading cause of cancer-related death in men (Jemal, A.,
2006, Supra; Hughes, C., et al., J. Clin. Pathol., 58: 673-684,
2005). To assess hSef expression in prostate tumors, 31 primary
prostatic adenocarcinomas, 5 cases of benign prostate hyperplasia
(BPH), as well as 4 examples of morphologically normal prostate
tissue were screened. Grading of cancer specimen is listed in Table
4, including 4 low grade [Gleason Grade (GG) 6], 10 intermediate
grade (GG7) and 17 high-grade (GG8-10) tumors. Representative
results shown in FIGS. 18a-f indicated that hSef is highly
expressed in the glandular epithelium, and to a much lesser extent
in stromal cells, of the normal prostate gland (FIG. 18a). Its
expression in the glandular epithelium of 4/5 BPH cases was
markedly decreased (FIG. 18b), and was lost in the fifth BPH case.
In 77.5% of the prostate cancer cases hSef expression was either
lost ( 16/31 cases, FIGS. 18c, e-f) or was markedly reduced ( 8/31
cases, FIG. 18d). Only 3 of these 24 cases were from low grade
tumors. Moderate hSef levels were observed in only 2 tumor samples
of low and an intermediate grade, respectively. In the remaining
tumor cases ( 5/31) hSef signal was heterogeneous. While part of
the tumor was negative other parts revealed moderate or low
expression (FIG. 18c and Table 4). These observations indicated
that a fraction of prostate malignancies harbored higher hSef
expression levels than BPH. Furthermore, they showed that hSef
expression is down-regulated in a significant fraction of prostate
cancers. TABLE-US-00004 TABLE 4 Summary of hSef expression in
ovarian carcinomas, thyroid tumors and prostate tumors Expression
Level Strong Histological type N (%) Moderate Low Negative Heteroa
Ovarian Tumors Serous papillary 4 1 3 adenocarcinoma/grade I grade
II 11 3 4 4 grade III 17 1 5 11 Others (a) 11 1 1 5 4 Summary of
primary 43 2 5 17 19 ovarian tumors (100%) (5%) (12%) (38%) (45%)
Metastasis from other 10 1 9 organs (100%) (10%) (90%) Thyroid
Tumors Papillary carcinoma 8 2 1 5 Follicular carcinoma 8 1 7
Summary of 16 3 1 12 carcinoma cases (100%) (19%) (6%) (75%)
Prostate Tumors BPH 5 4 1 Prostatic adenocarcinoma /G6 4 2 1 1 /G7
10 2 2 5 1 /G8-10 17 4 10 3 Summary of 31 2 8 16 5 adenocarcinoma
cases (100%) (6%) (26%) (52%) (16%) Table 4 - Summary of hSef
expression levels in ovarian, prostate and thyroid tumors.
Expression levels in the tumors were compared to hSef expression in
the epithelial cells of the corresponding normal tissues which was
scored very strong. For ovarian tumors levels are relative to those
observed in the in normal OSE and fallopian tube epithelium (3
cases). For thyroid, relative to expression in follicular cells (3
cases), and for prostate relative to the level observed in #
morphologically normal glandular epithelium (4 cases). Signal
intensity score was determined as described under Materials and
Methods. The secondary ovarian tumor positive for hSef expression
was a Krukenberg tumor (1/6 cases). The remaining secondary tumors
were 3 colon and 1 breast carcinoma cases. Other ovarian tumors (a)
include low grade transitional cell (1 case), and endometrioid (1)
carcinoma, and high grade mucinous (3), squamous (1), clear cell
(2), # un-differentiated (2), and small cell (1) carcinoma.
[0286] hSef is downregulated in four carcinoma types--A summary of
hSef levels in the primary tumors is shown in Table 5, hereinbelow.
Down regulation was observed in 95% ( 151/158) of these tumors. In
65% of the cases hSef signal was absent or extremely low, and in
22% of the cases hSef signal was weak. The remaining 8% of the
cases displayed 3-5 fold reduced hSef signal. Of the negative
cases, 98% were from intermediate and high-grade tumors. The cases
where hSef signal was relatively strong (5%), were from low grade
tumors. The marked down regulation of hSef expression in the four
carcinoma types, suggest that loss of hSef expression may be a
common theme in human carcinomas. TABLE-US-00005 TABLE 5 Carcinoma
grade Expression Low (%) Intermediate (%) High (%) Total cases (%)
level N = 22 N = 75 N = 61 N = 158 strong 7 (32) none none N = 7
(5) moderate 3 (14) 6 (8) 4 (7) N = 13 (8) low 10 (45) 9 (12) 16
(26) N = 35 (22) Negative 2 (9) 60 (80) 41 (67) N = 103 (65) Table
5 - Summary of hSef expression levels in the various human primary
carcinoma types according to tumor grade. Low grade includes all
tumors that were classified as grade I carcinoma and prostate
adenocarcinoma GG6. Intermediate grade includes all tumors
classified as grade II, 7/8 cases follicular carcinoma of the
thyroid, and prostate adenocarcinoma GG7. High grade includes all
grade III carcinomas, and prostatic adenocarcinoma GG8-10. #
Prostatic carcinoma cases with heterogeneous expression pattern
were included in the moderate expression level group. Chi square
test indicated that association of hSef down-regulation and tumor
progression was statistically significant (p .ltoreq. 0.001).
Example 9
Inhibition of Human Sef by RNA Interference Facilitates the Growth
of Cervical Carcinoma
[0287] As is shown in Table 2 and is described in Example 7,
hereinabove, cells transfected with the hSef-a or the hSef-b
expression vector formed 95% less colonies relative to empty
control vector. In addition, as is shown in FIGS. 15-18 and is
described in Example 8, hereinabove, the expression level of hSef
is downregulated in a variety of human carcinomas as compared with
the high expression in the corresponding normal epithelial cells.
These results strongly suggest a role for hSef in constraining
proliferation. Thus, it is expected that suppression of endogenous
hSef expression would accelerate tumor cell growth. To test this
hypothesis, the present inventor has employed the RNAi approach, as
follows.
[0288] Materials and Experimental Methods
[0289] Generation of hsef silencing constructs--The Whitehead siRNA
Selection Web Server and Oligoengine shockwave program were
employed for prediction of homologous hSef-a RNA oligonucleotides
(19 nucleotides). Three test sequences and one control sequence
were designed as follows: shRNA 1, forward, 5'-GTCGGAGGGAAGACAGTGC
(SEQ ID NO:23) ; reverse, 5'-GCACTGTCTTCCCTCCGAC (SEQ ID NO:24);
shRNA 2, forward, 5'-GCATGTGATTGCTGACGCC (SEQ ID NO:25); reverse,
5'-GGCGTCAGCAATCACATGC (SEQ ID NO:26). shRNA 3, forward,
5'-AGCAGGAGCAAACTACAGA (SEQ ID NO:27); reverse,
5'-TCTGTAGTTTGCTCCTGCT (SEQ ID NO:28). Control, forward,
5'-CGTGACAGAAGGGAGGCTG (SEQ ID NO:29); reverse,
5'-CAGCCTCCCTTCTGTCACG (SEQ ID NO:30). shRNA 1 in reverse
orientation was used as control. The 3' and 5' end of the
oligonucleotide primers were adapted for cloning into the BglII and
HindIII sites of pSUPER. To generate shRNAs, equimolar amounts of
complementary sense and antisense strands were mixed, annealed and
ligated into pSUPER digested with BglII/HindIII. Positive clones
were sequenced to ensure accuracy of RNAi.
[0290] Cell Culture, transfection methods and colony suppression
assay--as described in Example 7, hereinabove.
[0291] RNA interference--For hSef RNA interference, the efficiency
of hSef silencing was initially tested by co-transfecting an hSef
expression vector individually with each shRNA construct into
HEK-293 cells, using previously described transfection protocol
(Preger, 2004, Supra). Each Sef shRNA, but not the control shRNA or
empty pSUPER vector, reduced hSef protein levels when compared to
cells transfected with hSef construct alone (data not shown).
Subconfluent cultures of HeLa cells were then transfected with each
shRNA vector, a combination of the three hSef shRNA constructs (1.5
.mu.g each) or the control shRNA construct, together with pCDNA 3.1
(for selection). Following selection with 0.5 mg/ml G418, mass
cultures were tested for the reduction of endogenous hSef RNA. The
most efficient reduction was observed with cells transfected with
the combination of constructs. These cells were subsequently used
for future studies.
[0292] Proliferation assay--The assay was performed as previously
described (Shaoul, E., et al., Oncogene, 10: 1553-1561, 1995).
Briefly, Hela cells stably expressing hSef sh-RNA or control sh-RNA
were seeded into 24 well microtiter plates (2.5.times.10.sup.4
cells/well) in DMEM containing 10% FCS. The following day, cells
were washed 3 times with DMEM, and grown in DMEM alone or in the
presence of desired concentrations of growth factors. Fresh growth
factors were added every other day, and viable cells were counted
on day 5 of incubation. Each data point was performed in duplicates
or triplicates and each experiment was repeated at least 3
times.
[0293] Experimental Results
[0294] Downregulation of hsef enhances proliferation of HeLa
cervical carcinoma cells--The pSUPER system for RNA interference
was utilized to stably express hSef sh-RNA in HeLa cervical
carcinoma cells. RT-PCR analysis demonstrated that hSef RNA levels
were substantially reduced in cells stably expressing hSef sh-RNA,
but not in cells expressing the control sh-RNA (FIG. 19a).
Proliferation rate of the transfected cells in serum free
conditions (SFM) or in the presence of EGF (20 ng/ml) or FGF1 (10
or 20 ng/ml), was determined. The results clearly demonstrate that
hSef silencing enhances proliferation of HeLa cells by 2-4 folds in
serum-free conditions, and following exogenous ligand stimulation
(FIG. 19b). These results establish that endogenous hSef exerts a
growth constraining effect that is removed upon hSef downregulation
in tumor cells.
[0295] Analysis and Discussion
[0296] Subversion of physiological RTK signaling is a common
mechanism by which cancer cells gain uncontrolled growth potential
(Blume-Jensen, P. and Hunter, T. Oncogenic kinase signalling,
Nature., 411: 355-365, 2001) Although there is extensive evidence
implicating oncogenic RTK activation by overexpression, mutation
and autocrine ligand expression in human cancer, less is known
about abrogation of negative regulatory constraints resulting in
chronic activation of RTK-mediated signaling pathways. Sef is a
novel inhibitor of RTK-mediated signaling whose role in the
neoplastic process has not been established. The results described
in Examples 7-9 hereinabove provide the first comprehensive
expression analysis of hSef in different human carcinoma types of
high incidence, as well as functional studies that clearly indicate
a role for hSef in the neoplastic process. These findings
demonstrate that hSef is highly expressed in epithelial cells of
normal human breast, ovary, thyroid and prostate glands. In
striking contrast, hSef expression was significantly down-regulated
in 95% of malignancies originating from these epithelia overall. A
tumor-specific decrease comprised loss of hSef expression in 65%
and substantial reduction in additional 22% of tumors. Among the
remaining tumors, 8% showed moderate reduction in hSef expression,
and merely 5% displayed a strong hSef signal approaching expression
levels of normal epithelium. The small subset of tumors displaying
strong hSef expression was exclusively from low-grade tumors,
accounting for only one third of tumors of this grade ( 7/21
cases). In contrast, 98% of malignancies devoid of hSef expression
were intermediate or high-grade tumors (summary in Table 5,
hereinabove). The marked down-regulation of hSef expression in all
four carcinoma types implies that loss of hSef expression may be a
common mechanism in human epithelial neoplasia. Moreover,
association of hSef loss of expression with tumor grade indicates
that hSef down-regulation relates to the aggressiveness of the
tumor cell in vivo.
[0297] The extent of hSef loss of expression varied among the
different tumor types studied. Accordingly, hSef loss of expression
was observed in 83% of breast carcinoma, while 75% of a smaller
cohort of thyroid tumors lacked hSef expression. By comparison, the
percentage of ovarian and prostate malignancies devoid of hSef
expression was 45% and 52%, respectively. The different cancer
types varied also with respect to kinetics of hSef loss of
expression during tumor progression. In ovary, 36% intermediate
grade and 50% high grade primary ovarian carcinomas lost hSef
expression. In prostate cancer 50% of intermediate grade and 59% of
high grade tumors did not express hSef in agreement with Darby et
al., (Darby, S., et al., Oncogene., 25:4122-7, 2006). In contrast,
in breast and thyroid carcinomas the majority of intermediate grade
tumors were already negative for hSef expression (93%, and 100%,
respectively). These observed variations in the extent and kinetics
of hSef loss of expression during tumor progression may reflect
differences in organ or tissue specific mechanisms utilized for
silencing hSef expression.
[0298] The current study provided compelling evidence that hSef may
function as a tumor suppressor. First, hSef transcripts are highly
expressed in the normal epithelium of the four tissue types
analyzed. Second, significant down-regulation of hSef expression
occurred in primary carcinomas derived from these epithelial
tissues. Third, overexpression of either hSef isoform in human
breast cancer cells inhibited colony formation. Finally, lowering
hSef expression in cervical carcinoma cells by RNA interference
significantly augmented their proliferation rate in response to EGF
and FGF. These results combined with the known capacity of
mammalian Sefs to inhibit two major pathways for transduction of
oncogenic signals including RAS/MAPK and PI 3-K (Preger, E., 2004,
Supra; Xiong, S., et al., J Biol Chem., 278:50273-50282, 2003;
Torii, S., et al., Dev. Cell, 7: 33-44, 2004; Yang, X., et al., J.
Biol. Chem., 279: 38099-38102, 2004; Ziv, I., et al., Human Sef-a
isoform utilizes different mechanisms to regulate FGFR signaling
pathways and subsequent cell fate. In: Anonymous 2006; Kovalenko,
D., et al., J. Biol. Chem., 278: 14087-14091, 2003), strongly
support a role for hSef in negatively regulating cellular growth
and clearly indicate a role for hSef loss of function in the
neoplastic process.
[0299] A characteristic of feedback antagonists of RTK signaling
involves induction of expression by the same pathway they inhibit
(Niehrs, C. and Meinhardt, H. Modular feedback, Nature, 417: 35-36,
2002). Consistently, induction of Sef expression by FGFs in
zebrafish or chick embryos (Tsang, M., et al., Nat. Cell Biol., 4:
165-169, 2002; Furthauer, M., et al., Nat. Cell Biol., 4: 170-174,
2002; Harduf, H., et al., Dev. Dyn., 233: 301-312, 2005). In
addition, both EGF and FGFs induced hSef expression in vitro
(unpublished results). The current findings revealed downregulation
of hSef expression in malignancies in which expression of various
ligands and receptors of the EGF and FGF families is known to be
elevated (Normanno, N., et al., Curr. Drug Targets., 6: 243-257,
2005; Furthauer, M., et al., Nat. Cell Biol., 4: 170-174, 2002;
Steele, I. A., et al., Oncogene., 20: 5878-5887, 2001). Therefore,
specific mechanisms must prevent induction of hSef by these growth
factor/RTK pathways in cancer cells. Such mechanisms may involve
transcriptional repression, decreased RNA stability, DNA
methylation or deletion. The hSef gene maps to chromosome 3p14,
where defined genetic and epigenetic alterations have been
identified in a number of human malignancies, including lung and
breast cancer (Matsumoto, S., et al., Genes Chromosomes. Cancer.,
20: 268-274, 1997; Kovacs, G., et al., Int. J. Cancer, 43: 422-427,
1989; Pathak, S., et al., Science, 217: 939-941, 1982). In this
context, it is noteworthy that we have identified two CpG islands
that overlap with the first exon of hSef-a and hSef-b (unpublished
observation), raising the possibility that hSef methylation may be
one mechanism involved in loss of hSef expression in human
carcinomas.
[0300] In summary, these results strongly indicate that hSef
down-regulation might be a general characteristic of human cancer
and suggest a role for hSef loss of function in the neoplastic
process. Further insights into the mechanism(s) underlying hSef
loss of expression in human malignancy would not only advance the
understanding of tumor pathogenesis, but also facilitate the design
of novel therapeutic strategies based on upregulating hSef in human
carcinomas.
Example 10
Administration of a Human Sef Upregulating Agent to Animal Models
Induced to Bear Cancerous Tumors
[0301] To test the effect of upregulation of Sef on the inhibition
of solid tumor growth in vivo, the present inventor has designed
the following experimental approaches.
[0302] Tumor formation in transgenic mice overexpressing an
oncogene--A transgenic mouse model for cancer (e.g., breast cancer)
such as the erb model (Shah N., et al., 1999, Cancer Lett. 146:
15-2; Weistein E J., et al., 2000, Mol. Med. 6: 4-16) or MTV/myc
model (Stewart T A et al., 1984, Cell, 38: 627-637), the c-myc
model (Leder A., et al., 1986, Cell, 45:485-495), v-Ha-ras or c-neu
model (Elson A and Leder P, 1995, J. Biol. Chem. 270: 26116-22) can
be used to test the ability of hSef to suppress tumor growth in
vivo.
[0303] Tumor formation in mice administered with cancerous cell
lines--For the formation of solid tumors, athymic mice can be
injected with human or animal (e.g., mouse) cancerous cells such as
those derived from breast cancer, ovarian cancer, prosate cancer or
thyroid cancer, and following the formation of cancerous tumors the
mice can be subjected to intra-tumor and/or systemic administration
of an agent capable of upregulating hSef expression level and/or
activity (e.g., by overexpression of hSef).
[0304] The Following Cell Lines (Provided with Their ATCC Accession
Numbers) Can be Used for Each Type of Cancer Model:
[0305] For Breast Cancer:
[0306] Human breast cancer cell lines--MDA-MB-453 (ATCC No.
HTB-131), MDA-MB-231 (ATCC No. HTB-26), BT474 (ATCC No. HTB-20),
MCF-7 (ATCC No. HTB-22), MDA-MB-468, (for additional cell lines see
http://www.path.cam.ac.uk/.about.pawefish/index.html);
[0307] For Ovarian Cancer:
[0308] Human ovarian cancer cell lines--SKOV3 (ATCC No. HTB-77),
OVCAR-3 HTB-161), OVCAR-4, OVCAR-5, OVCAR-8 and IGROV1;
[0309] For Prostate Cancer:
[0310] Human prostate cancer cell lines--DU-145 (ATCC No. HTB-81),
PC-3 (ATCC No. CRL-1435);
[0311] For Thyroid Cancer:
[0312] Human derived thyroid cancer cell lines--FTC-133, K1, K2,
NPA87, K5, WRO82-1, AR089-1, DRO81-1;
[0313] For Lung Cancer:
[0314] Mouse lung carcinoma LL/2 (LLC1) cells (Lewis lung
carcinoma)--These cells are derived from a mouse bearing a tumor
resulting from an implantation of primary Lewis lung carcinoma. The
cells are tumorigenic in C57BL mice, express H-2b antigen and are
widely used as a model for metastasis and for studying the
mechanisms of cancer chemotherapeutic agents (Bertram J S, et al.,
1980, Cancer Lett. 11: 63-73; Sharma S, et al. 1999, J. Immunol.
163: 5020-5028).
[0315] For Melanoma:
[0316] Mouse B16-F10 cells (Melanoma)--The cells are derived from
mouse (C57BL/6J) bearing melanoma (Briles E B, et al., 1978, J.
Natl. Cancer Inst. 60: 1217-1222).
[0317] Culturing conditions of cancerous cells--The cancerous cells
can be cultured in a tissue culture medium such as the DMEM with 4
mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate and
4.5 g/L glucose, supplemented with 10% fetal calf serum (FCS),
according to known procedures (e.g., as described in the ATCC
protocols).
[0318] Tumor formation in animal models by administration of
cancerous cells--Athymic nu/nu mice (e.g., female mice) can be
purchased from the Jackson Laboratory (Bar Harbor, Me.). Tumors can
be formed by subcutaneous (s.c.) injection of cancerous cells
(e.g., 2.times.10.sup.6 cells in 100 .mu.l of PBS per mouse).
Tumors are then allowed to grow in vivo for several days (e.g.,
6-14 days) until they reach a detectable size of about 0.5 cm in
diameter. It will be appreciated that injection of cancerous cells
to an animal model can be at the organ from which the cell line is
derived (e.g., mammary tissue for breast cancer, ovary for ovarian
cancer) or can be injected at an irrelevant tissue such as the rear
leg of the mouse.
[0319] Modes of administration of hSef--To test the effect of hSef
on inhibition of tumor growth, hSef is administered to the animal
model bearing the tumor either locally at the site of tumor or
systemically, by intravenous injection of infusion, via, e.g., the
tail vein. The time of Sef administration may vary from immediately
following injection of the cancerous cell line (e.g., by systemic
administration) or at predetermined time periods following the
appearance of the solid tumor (e.g., to the site of tumor
formation, every 3 days for 3-10 times as described in Ugen K E et
al., Cancer Gene Ther. Jun. 9, 2006; [Epub ahead of print]).
[0320] Ectopic expression (overexpression) of hsef in solid
tumors--Administration of hSef can be effected using a nucleic acid
construct designed to express hSef coding sequence (e.g., a viral
vector), naked pDNA and/or hSef liposomes, as follows.
[0321] Viral vectors--Overexpression of hSef can be effected using
viral expression vectors as described hereinabove [e.g., the
recombinant adeno-associated virus 2 (AAV) as described in
Mahendra, 2005 (Supra), SV40-based as described in Kimchi-Sarfaty
C, and Gottesman M M, 2004, Curr. Pharm. Biotechnol. 5: 451-8;
retroviruses such as Molony murine leukemia virus (Mo-MuLV); and
lentiviruses (Amado R G, Chen I S., 1999, Science. 285: 674-6].
Briefly, null adenovirus (i.e., an adenovirus vector lacking an
insert) or adenovirus expressing either hSef-a (SEQ ID NO:10) or
hSef-b (SEQ ID NO:4) or hSef-c (SEQ ID NO:8) can be amplified and
titered in host cells (e.g., bone marrow cells derived from the
animal) which are further administered back to the animal (i.e., ex
vivo gene therapy) essentially as described elsewhere (He L., Yu J.
X., et al., Cancer Res., 58: 4238-4244, 1998). Alternatively, the
adenovirus vector expressing hSef-a or hSef-b can be administered
directly to the individual (e.g., animal model) using systemic or
local modes of administrations (i.e., in vivo gene therapy).
[0322] Adenovirus preparations of about 8.times.10.sup.10 particles
of virus/dose of the null, hSef-a or hSef-b coding sequences are
administered intratumoral or peritumoral in a volume of about 100
.mu.l. PBS is injected as a negative control. Doses can be every
other day for total of four doses to mice bearing tumors. For
further details see Guang-Liang Jiang and Shi Huang, 2001, Cancer
Research 61: 1796-1798.
[0323] Liposome delivery system--Liposomes can be used for in vivo
delivery of hSef polynucleotides to target cells. For example, the
cationic lipid formulation 3 beta
[N-(N',N'-Dimethylaminoethane)-Carbamoyl] Cholesterol (DC-Chol) is
a non-viral delivery agent which can be used to target of hSef into
cells of interest (e.g., cancerous cells). For example, allogeneic
and xenogeneic MHC DNA-liposome complexes were successfully
employed in a phase I study of immunotherapy of cutaneous
metastases of human carcinoma using the DC-Chol/DOPE cationic
liposomes (see for example, Hui K M, Ang P T, Huang L, Tay S K.,
1997, Gene Ther. 1997, 4(8):783-90; Serikawa T., et al., 2006,
Journal of Controlled Release, Apr. 26, 2006; [Epub ahead of
print]).
[0324] The hSef liposomes can be administered directly into the
tumor cells or can be administered intravenously and be directed to
the cells-of-interest using a cell specific recognition moiety such
as a ligand, antibody or receptor capable of specifically binding
to the cell-of-interest. For example, in order to direct the
hSef-liposomes to cancerous cells of an epithelial origin (e.g.,
breast cancer cells), the liposomes can include a ligand that can
specifically recognize the cancereous cells due to overexpression
of the receptor for this specific ligand. For example, one such
ligand can be the keratinocyte growth factor (KGF or FGF7) molecule
which is specific for cells of epithelial origin. Thus, KGF can be
directed to tumors such as endometrial carcinoma or pancreatic
carcinoma where the KGF receptor is overexpressed (Visco, V., et
al., 1999, Expression of keratinocyte growth factor receptor
compared with that of epidermal growth factor receptor and erbB-2
in endometrial adenocarcinoma, Int. J. Oncol., 15: 431-435;
Siegfried, S., et al., 1997, Distinct patterns of expression of
keratinocyte growth factor and its receptor in endometrial
carcinoma, Cancer, 79: 1166-1171). Similarly other ligands such as
EGF can be used to target lyposomes into tumors where the EGF
receptor is overexpressed such as glyomas and endometrial
carcinomas (for a review see: Normanno, N., et al., 2005, The ErbB
receptors and their ligands in cancer: an overview, Curr. Drug
Targets. 6:243-257). It should be noted, that since malignant cells
of epithelial origin overexpress the KGF receptor, they are more
susceptible to hSef-liposome treatment than other non-malignant
cells. To this end, the present inventor has prepared KGF which can
be attached to the liposomes.
[0325] Additionally or alternatively, targeting of the liposome to
specific cells can be performed by antibodies essentially as
described in Dass C R. and Choong P F, J Control Release. May 9,
2006; [Epub ahead of print]. For example, a single chain FV
antibody against the KGF receptor can be used to target the hSef
liposome to cancerous cells of epithelial origin.
[0326] Naked nucleic acids--Naked DNA [e.g., naked plasmid DNA
(pDNA)] is an attractive simple, non-viral vector which can easily
be produced in bacteria and manipulated using standard recombinant
DNA techniques. It does not induce antibody response against itself
(i.e., no anti-DNA antibodies generated) and enables long-term gene
expression even without chromosome integration. Naked hSef DNA can
be introduced by intravascular and electroporation techniques as
described in Wolff J A, Budker V, 2005, Adv. Genet. 54: 3-20.
Alternatively, naked hSef DNA can be administered locally
(intratumorally) followed by eletroporation as described for the
DNA plasmid expressing interleukin-15 (pIL-15) which was
administered into melanoma tumors in mice and induced complete
tumor regression in 37% of the treated mice [Ugen K E, 2006
(Supra)]. Still alternatively, naked hSef DNA can be administered
in vivo by jet injection essentially as described in Walther W, et
al., 2004, Mol. Biotechnol. 28: 121-8. Still alternatively, naked
hSef DNA can be administered into epidermis cells via DNA-coated
gold particles as described in Dean H J, 2005, Expert Opin Drug
Deliv. 2: 227-36. Still alternatively, naked hSef DNA can be
administered to cancerous cells via cavitation bubbles which induce
transient membrane permeabilization (sonoporation) on a single cell
level [using low frequency sonication (kilohertz frequencies),
lithotripter shockwaves, HIFU, and even diagnostic ultrasound
(megahertz frequencies)]. Cavitation initiation and control can be
enhanced by cavitation nucleation agents, such as an ultrasound
contrast agent [for further details see Miller D L, et al., 2002,
Somat Cell Mol. Genet. 27:115-34; using e.g., the Sonitron 2000
sonoporation system (Sonidel Limited, Dublin, Republic
Ireland).
[0327] Evaluation of solid tumor inhibition--Tumor sizes are
measured two to three times a week. Tumor volumes are calculated
using the length and width of the tumor (in millimeters). The
effect of hSef treatment can be evaluated by comparing the tumor
volume using statistical analyses such as Student's t test. In
addition, histological analyses can be performed using markers
typical for each type of cancer.
[0328] Altogether, once the tumors are formed, the agent capable of
upregulating hSef expression level and/or activity is administered
to the individual in need thereof, e.g., the animal model bearing
the tumor, either locally or systemically, and the effect of the
agent on tumor growth is detected using methods known in the
art.
Example 11
Formation of an Animal Model with Conditional Upregulation of
Sef
[0329] To test the ability of hSef to inhibit the growth of solid
tumor, a conditioned animal model in which Sef expression is
upregulated in a spatial and a temporal manner following or
concomitant with tumor formation can be utilized. Mice with
conditioned expression of Sef can be subjected to in vivo formation
of tumors by overexpression of an oncogene at the tissue-of-choice
where Sef is expressed or by subjecting the tissue-of-choice to
carcinogenic agents, as follows.
[0330] Animal model with a spatial and a temporal expression of
hSef can be used to inhibit tumor growth by upregulation of Sef--A
transgenic mouse model where hSef is specifically expressed in a
certain tissue (e.g., breast or skin) and switches on hSef
expression at specific times during tumor growth can be designed.
Temporal expression of Sef can be achieved by a vector for
conditioned expression such the Tet-off/Tet-On expression systems
(Clontech Laboratories, Inc). For example, when the Tet-Off
expression system is used, hSef expression (preferably in a
specific tissue) is upregulated in the absence of tetracycline
(doxycycline). On the other hand, hSef expression (in the specific
tissue) can initiate following the appearance of a tumor in a
transgenic mouse expressing erb and transfected with a Tet-On
expression system. In this mouse, once the breast cancer tumors are
detectable (e.g., using ultrasound), the mouse can be treated with
tetracycline which activates the expression of hSef-Tet-On
expression system. Overexpression of hSef will therefore result in
inhibiting tumor growth and treatment of cancer.
[0331] Generation of a mouse model with spatial and a temporal
expression of Sef in which an oncogen is expressed in a tissue
specific manner--To generate a mouse model in which hSef expression
is not only conditioned but also tissue specific, the tet system
can be used, as follows. The tTA (tet transactivator) expression is
controlled under a tissue specific promoter. For this purpose a
transgenic mouse is generated in which the expression of hSef is
under the control of the tTa. Then another mouse model is
generated, in which the oncogene--of choice (e.g., erb) that create
tumors is chosen such that it induces the tumors in one of the
sites of interest (e.g., breasr, skin). This mouse is then mated
with the first mouse where Sef-tTa expression is under the control
of a tissue-specific promoter and kept under conditions that hSef
expression is silenced. At different time intervals during tumor
development, hSef can be switched on, and then, the effect of its
expression can be tested. It is expected that that hSef will
suppress or even completely eradicate the tumor.
[0332] Generation of a mouse model with spatial and a temporal
expression of Sef in which tumors are formed due to exposure to
carcinogens--A transgenic hSef mouse under the control of tTa is
mated with a mouse of choice where the tTa itself is preferably
tissue specific. This mouse will be grown under conditions that
silence hSef. Such a mouse will be treated with carcinogens to
develop tumors in specific sites [e.g., dimethyl benzanthracene
(DMBA) and tetradecanoyl-phorbol acetate (TPA) for skin tumors
(Hecker E. Toxicol Pathol. 1987;15(2):245-58)]. hSef expression
will be switiched on at different time intervals during tumor
progression and the effect of this expression can be followed. It
is expected that hSef will be able to suppress tumor growth or to
eradicate it.
[0333] For further description of animal models using conditioned
expression of the gene-of-interest (e.g., Sef) see Takashi M., et
al., 2004, Mol. Carcinogenesis 40: 189-200; Gunther E J., et al.,
2002, FASEB, 16: 283-292; Miyazaki S., et al., 2005, Biochem.
Biophys. Res. Commun., 338: 1083-8; Kistner A., et al., 1996, Proc.
Natl. Acad. Sci. 93: 10933-10938; which are incorporated herein by
references.
[0334] Altogether, the experimental approaches described in
Examples 10 and 11, hereinabove can be used to test the ability of
the Sef upregulating agents of the present invention in inhibiting
the growth of solid tumor in vivo.
[0335] It is appreciated that certain features of the invention,
which are, for clarity, described in the context of separate
embodiments, may also be provided in combination in a single
embodiment. Conversely, various features of the invention, which
are, for brevity, described in the context of a single embodiment,
may also be provided separately or in any suitable
subcombination.
[0336] Although the invention has been described in conjunction
with specific embodiments thereof, it is evident that many
alternatives, modifications and variations will be apparent to
those skilled in the art. Accordingly, it is intended to embrace
all such alternatives, modifications and variations that fall
within the spirit and broad scope of the appended claims. All
publications, patents and patent applications mentioned in this
specification are herein incorporated in their entirety by
reference into the specification, to the same extent as if each
individual publication, patent or patent application was
specifically and individually indicated to be incorporated herein
by reference. In addition, citation or identification of any
reference in this application shall not be construed as an
admission that such reference is available as prior art to the
present invention.
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(Additional References are Cited in the Text)
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Sequence CWU 1
1
31 1 25 DNA Artificial sequence Single strand DNA oligonucleotide 1
agtggcaatg cttagactct ttcgt 25 2 25 DNA Artificial sequence Single
strand DNA oligonucleotide 2 gcgtgccaga cagagtgcta ggcat 25 3 36
DNA Artificial sequence Single strand DNA oligonucleotide 3
gaggatccaa gctttgttac aaaggggcga ccgcgt 36 4 2214 DNA Homo sapiens
4 gcgtgccaga cagagtgcta ggcatggggg cagaggtgaa tcagatgaca gccacctctc
60 accacgagga gtggctgaaa gtgtgactgg actacaggca atcctggcct
tggcagggag 120 tggggccagc cagcagaaac agtgggctgt acaacatcac
cttcaaatat gacaattgta 180 ccacctactt gaatccagtg gggaagcatg
tgattgctga cgcccagaat atcaccatca 240 gccagtatgc ttgccatgac
caagtggcag tcaccattct ttggtcccca ggggccctcg 300 gcatcgaatt
cctgaaagga tttcgggtaa tactggagga gctgaagtcg gagggaagac 360
agtgccaaca actgattcta aaggatccga agcagctcaa cagtagcttc aaaagaactg
420 gaatggaatc tcaacctttc ctgaatatga aatttgaaac ggattatttc
gtaaaggttg 480 tcccttttcc ttccattaaa aacgaaagca attaccaccc
tttcttcttt agaacccgag 540 cctgtgacct gttgttacag ccggacaatc
tagcttgtaa acccttctgg aagcctcgga 600 acctgaacat cagccagcat
ggctcggaca tgcaggtgtc cttcgaccac gcaccgcaca 660 acttcggctt
ccgtttcttc tatcttcact acaagctcaa gcacgaagga cctttcaagc 720
gaaagacctg taagcaggag caaactacag agatgaccag ctgcctcctt caaaatgttt
780 ctccagggga ttatataatt gagctggtgg atgacactaa cacaacaaga
aaagtgatgc 840 attatgcctt aaagccagtg cactccccgt gggccgggcc
catcagagcc gtggccatca 900 cagtgccact ggtagtcata tcggcattcg
cgacgctctt cactgtgatg tgccgcaaga 960 agcaacaaga aaatatatat
tcacatttag atgaagagag ctctgagtct tccacataca 1020 ctgcagcact
cccaagagag aggctccggc cgcggccgaa ggtctttctc tgctattcca 1080
gtaaagatgg ccagaatcac atgaatgtcg tccagtgttt cgcctacttc ctccaggact
1140 tctgtggctg tgaggtggct ctggacctgt gggaagactt cagcctctgt
agagaagggc 1200 agagagaatg ggtcatccag aagatccacg agtcccagtt
catcattgtg gtttgttcca 1260 aaggcatgaa gtactttgtg gacaagaaga
actacaaaca caaaggaggt ggccgaggct 1320 cggggaaagg agagctcttc
ctggtggcgg tgtcagccat tgccgaaaag ctccgccagg 1380 ccaagcagag
ttcgtccgcg gcgctcagca agtttatcgc cgtctacttt gattattcct 1440
gcgagggaga cgtccccggt atcctagacc tgagtaccaa gtacagactc atggacaatc
1500 ttcctcagct ctgttcccac ctgcactccc gagaccacgg cctccaggag
ccggggcagc 1560 acacgcgaca gggcagcaga aggaactact tccggagcaa
gtcaggccgg tccctatacg 1620 tcgccatttg caacatgcac cagtttattg
acgaggagcc cgactggttc gaaaagcagt 1680 tcgttccctt ccatcctcct
ccactgcgct accgggagcc agtcttggag aaatttgatt 1740 cgggcttggt
tttaaatgat gtcatgtgca aaccagggcc tgagagtgac ttctgcctaa 1800
aggtagaggc ggctgttctt ggggcaaccg gaccagccga ctcccagcac gagagtcagc
1860 atgggggcct ggaccaagac ggggaggccc ggcctgccct tgacggtagc
gccgccctgc 1920 aacccctgct gcacacggtg aaagccggca gcccctcgga
catgccgcgg gactcaggca 1980 tctatgactc gtctgtgccc tcatccgagc
tgtctctgcc actgatggaa ggactctcga 2040 cggaccagac agaaacgtct
tccctgacgg agagcgtgtc ctcctcttca ggcctgggtg 2100 aggaggaacc
tcctgccctt ccttccaagc tcctctcttc tgggtcatgc aaagcagatc 2160
ttggttgccg cagctacact gatgaactcc acgcggtcgc ccctttgtaa caaa 2214 5
739 PRT Homo sapiens 5 Met Ala Pro Trp Leu Gln Leu Cys Ser Val Phe
Phe Thr Val Asn Ala 1 5 10 15 Cys Leu Asn Gly Ser Gln Leu Ala Val
Ala Ala Gly Gly Ser Gly Arg 20 25 30 Ala Arg Gly Ala Asp Thr Cys
Gly Trp Arg Gly Val Gly Pro Ala Ser 35 40 45 Arg Asn Ser Gly Leu
Tyr Asn Ile Thr Phe Lys Tyr Asp Asn Cys Thr 50 55 60 Thr Tyr Leu
Asn Pro Val Gly Lys His Val Ile Ala Asp Ala Gln Asn 65 70 75 80 Ile
Thr Ile Ser Gln Tyr Ala Cys His Asp Gln Val Ala Val Thr Ile 85 90
95 Leu Trp Ser Pro Gly Ala Leu Gly Ile Glu Phe Leu Lys Gly Phe Arg
100 105 110 Val Ile Leu Glu Glu Leu Lys Ser Glu Gly Arg Gln Cys Gln
Gln Leu 115 120 125 Ile Leu Lys Asp Pro Lys Gln Leu Asn Ser Ser Phe
Lys Arg Thr Gly 130 135 140 Met Glu Ser Gln Pro Phe Leu Asn Met Lys
Phe Glu Thr Asp Tyr Phe 145 150 155 160 Val Lys Val Val Pro Phe Pro
Ser Ile Lys Asn Glu Ser Asn Tyr His 165 170 175 Pro Phe Phe Phe Arg
Thr Arg Ala Cys Asp Leu Leu Leu Gln Pro Asp 180 185 190 Asn Leu Ala
Cys Lys Pro Phe Trp Lys Pro Arg Asn Leu Asn Ile Ser 195 200 205 Gln
His Gly Ser Asp Met Gln Val Ser Phe Asp His Ala Pro His Asn 210 215
220 Phe Gly Phe Arg Phe Phe Tyr Leu His Tyr Lys Leu Lys His Glu Gly
225 230 235 240 Pro Phe Lys Arg Lys Thr Cys Lys Gln Glu Gln Thr Thr
Glu Met Thr 245 250 255 Ser Cys Leu Leu Gln Asn Val Ser Pro Gly Asp
Tyr Ile Ile Glu Leu 260 265 270 Val Asp Asp Thr Asn Thr Thr Arg Lys
Val Met His Tyr Ala Leu Lys 275 280 285 Pro Val His Ser Pro Trp Ala
Gly Pro Ile Arg Ala Val Ala Ile Thr 290 295 300 Val Pro Leu Val Val
Ile Ser Ala Phe Ala Thr Leu Phe Thr Val Met 305 310 315 320 Cys Arg
Lys Lys Gln Gln Glu Asn Ile Tyr Ser His Leu Asp Glu Glu 325 330 335
Ser Ser Glu Ser Ser Thr Tyr Thr Ala Ala Leu Pro Arg Glu Arg Leu 340
345 350 Arg Pro Arg Pro Lys Val Phe Leu Cys Tyr Ser Ser Lys Asp Gly
Gln 355 360 365 Asn His Met Asn Val Val Gln Cys Phe Ala Tyr Phe Leu
Gln Asp Phe 370 375 380 Cys Gly Cys Glu Val Ala Leu Asp Leu Trp Glu
Asp Phe Ser Leu Cys 385 390 395 400 Arg Glu Gly Gln Arg Glu Trp Val
Ile Gln Lys Ile His Glu Ser Gln 405 410 415 Phe Ile Ile Val Val Cys
Ser Lys Gly Met Lys Tyr Phe Val Asp Lys 420 425 430 Lys Asn Tyr Lys
His Lys Gly Gly Gly Arg Gly Ser Gly Lys Gly Glu 435 440 445 Leu Phe
Leu Val Ala Val Ser Ala Ile Ala Glu Lys Leu Arg Gln Ala 450 455 460
Lys Gln Ser Ser Ser Ala Ala Leu Ser Lys Phe Ile Ala Val Tyr Phe 465
470 475 480 Asp Tyr Ser Cys Glu Gly Asp Val Pro Gly Ile Leu Asp Leu
Ser Thr 485 490 495 Lys Tyr Arg Leu Met Asp Asn Leu Pro Gln Leu Cys
Ser His Leu His 500 505 510 Ser Arg Asp His Gly Leu Gln Glu Pro Gly
Gln His Thr Arg Gln Gly 515 520 525 Ser Arg Arg Asn Tyr Phe Arg Ser
Lys Ser Gly Arg Ser Leu Tyr Val 530 535 540 Ala Ile Cys Asn Met His
Gln Phe Ile Asp Glu Glu Pro Asp Trp Phe 545 550 555 560 Glu Lys Gln
Phe Val Pro Phe His Pro Pro Pro Leu Arg Tyr Arg Glu 565 570 575 Pro
Val Leu Glu Lys Phe Asp Ser Gly Leu Val Leu Asn Asp Val Met 580 585
590 Cys Lys Pro Gly Pro Glu Ser Asp Phe Cys Leu Lys Val Glu Ala Ala
595 600 605 Val Leu Gly Ala Thr Gly Pro Ala Asp Ser Gln His Glu Ser
Gln His 610 615 620 Gly Gly Leu Asp Gln Asp Gly Glu Ala Arg Pro Ala
Leu Asp Gly Ser 625 630 635 640 Ala Ala Leu Gln Pro Leu Leu His Thr
Val Lys Ala Gly Ser Pro Ser 645 650 655 Asp Met Pro Arg Asp Ser Gly
Ile Tyr Asp Ser Ser Val Pro Ser Ser 660 665 670 Glu Leu Ser Leu Pro
Leu Met Glu Gly Leu Ser Thr Asp Gln Thr Glu 675 680 685 Thr Ser Ser
Leu Thr Glu Ser Val Ser Ser Ser Ser Gly Leu Gly Glu 690 695 700 Glu
Glu Pro Pro Ala Leu Pro Ser Lys Leu Leu Ser Ser Gly Ser Cys 705 710
715 720 Lys Ala Asp Leu Gly Cys Arg Ser Tyr Thr Asp Glu Leu His Ala
Val 725 730 735 Ala Pro Leu 6 707 PRT Homo sapiens 6 Leu Asp Tyr
Arg Gln Ser Trp Pro Trp Gln Gly Val Gly Pro Ala Ser 1 5 10 15 Arg
Asn Ser Gly Leu Tyr Asn Ile Thr Phe Lys Tyr Asp Asn Cys Thr 20 25
30 Thr Tyr Leu Asn Pro Val Gly Lys His Val Ile Ala Asp Ala Gln Asn
35 40 45 Ile Thr Ile Arg Gln Tyr Ala Cys His Asp Gln Val Ala Val
Thr Ile 50 55 60 Leu Trp Ser Pro Gly Ala Leu Gly Ile Glu Phe Leu
Lys Gly Phe Arg 65 70 75 80 Val Ile Leu Glu Glu Leu Lys Ser Glu Gly
Arg Gln Cys Gln Gln Leu 85 90 95 Ile Leu Lys Asp Pro Lys Gln Leu
Asn Ser Ser Phe Lys Arg Thr Gly 100 105 110 Met Glu Ser Gln Pro Phe
Leu Asn Met Lys Phe Glu Thr Asp Tyr Phe 115 120 125 Val Lys Val Val
Pro Phe Pro Ser Ile Lys Asn Glu Ser Asn Tyr His 130 135 140 Pro Phe
Phe Phe Arg Thr Arg Ala Cys Asp Leu Leu Leu Gln Pro Asp 145 150 155
160 Asn Leu Ala Cys Lys Pro Phe Trp Lys Pro Arg Asn Leu Asn Ile Ser
165 170 175 Gln His Gly Ser Asp Met Gln Val Ser Phe Asp His Ala Pro
His Asn 180 185 190 Phe Gly Phe Arg Phe Phe Tyr Leu His Tyr Lys Leu
Lys His Glu Gly 195 200 205 Pro Phe Lys Arg Lys Thr Cys Lys Gln Glu
Gln Thr Thr Glu Met Thr 210 215 220 Ser Cys Leu Leu Gln Asn Val Ser
Pro Gly Asp Tyr Ile Ile Glu Leu 225 230 235 240 Val Asp Asp Thr Asn
Thr Thr Arg Lys Val Met His Tyr Ala Leu Lys 245 250 255 Pro Val His
Ser Pro Trp Ala Gly Pro Ile Arg Ala Val Ala Ile Thr 260 265 270 Val
Pro Leu Val Val Ile Ser Ala Phe Ala Thr Leu Phe Thr Val Met 275 280
285 Cys Arg Lys Lys Gln Gln Glu Asn Ile Tyr Ser His Leu Asp Glu Glu
290 295 300 Ser Ser Glu Ser Ser Thr Tyr Thr Ala Ala Leu Pro Arg Glu
Arg Leu 305 310 315 320 Arg Pro Arg Pro Lys Val Phe Leu Cys Tyr Ser
Ser Lys Asp Gly Gln 325 330 335 Asn His Met Asn Val Val Gln Cys Phe
Ala Tyr Phe Leu Gln Asp Phe 340 345 350 Cys Gly Cys Glu Val Ala Leu
Asp Leu Trp Glu Asp Phe Ser Leu Cys 355 360 365 Arg Glu Gly Gln Arg
Glu Trp Val Ile Gln Lys Ile His Glu Ser Gln 370 375 380 Phe Ile Ile
Val Val Cys Ser Lys Gly Met Lys Tyr Phe Val Asp Lys 385 390 395 400
Lys Asn Tyr Lys His Lys Gly Gly Gly Arg Gly Ser Gly Lys Gly Glu 405
410 415 Leu Phe Leu Val Ala Val Ser Ala Ile Ala Glu Lys Leu Arg Gln
Ala 420 425 430 Lys Gln Ser Ser Ser Ala Ala Leu Ser Lys Phe Ile Ala
Val Tyr Phe 435 440 445 Asp Tyr Ser Cys Glu Gly Asp Val Pro Gly Ile
Leu Asp Leu Ser Thr 450 455 460 Lys Tyr Arg Leu Met Asp Asn Leu Pro
Gln Leu Cys Ser His Leu His 465 470 475 480 Ser Arg Asp His Gly Leu
Gln Glu Pro Gly Gln His Thr Arg Gln Gly 485 490 495 Ser Arg Arg Asn
Tyr Phe Arg Ser Lys Ser Gly Arg Ser Leu Tyr Val 500 505 510 Ala Ile
Cys Asn Met His Gln Phe Ile Asp Glu Glu Pro Asp Trp Phe 515 520 525
Glu Lys Gln Phe Val Pro Phe His Pro Pro Pro Leu Arg Tyr Arg Glu 530
535 540 Pro Val Leu Glu Lys Phe Asp Ser Gly Leu Val Leu Asn Asp Val
Met 545 550 555 560 Cys Lys Pro Gly Pro Glu Ser Asp Phe Cys Leu Lys
Val Glu Ala Ala 565 570 575 Val Leu Gly Ala Thr Gly Pro Ala Asp Ser
Gln His Glu Ser Gln His 580 585 590 Gly Gly Leu Asp Gln Asp Gly Glu
Ala Arg Pro Ala Leu Asp Gly Ser 595 600 605 Ala Ala Leu Gln Pro Leu
Leu His Thr Val Lys Ala Gly Ser Pro Ser 610 615 620 Asp Met Pro Arg
Asp Ser Gly Ile Tyr Asp Ser Ser Val Pro Ser Ser 625 630 635 640 Glu
Leu Ser Leu Pro Leu Met Glu Gly Leu Ser Thr Asp Gln Thr Glu 645 650
655 Thr Ser Ser Leu Thr Glu Ser Val Ser Ser Ser Ser Gly Leu Gly Glu
660 665 670 Glu Glu Pro Pro Ala Leu Pro Ser Lys Leu Leu Ser Ser Gly
Ser Cys 675 680 685 Lys Ala Asp Leu Gly Cys Arg Ser Tyr Thr Asp Glu
Leu His Ala Val 690 695 700 Ala Pro Leu 705 7 2339 DNA Homo sapiens
7 agcggattcg ctcttctttt cctccgggaa aagaaacggg aagtggccgt gggccggtga
60 attccgtgta gtggccaagc ttgttccaaa gagggggagg tgttgacagt
ctcttgccca 120 ctgaagcgtg ccagacagag tgctaggcat gggggcagag
gtgaatcaga tgacagccac 180 ctctcaccac gaggagtggc tgaaagtgtg
actggactac aggcaatcct ggccttggca 240 gggagtgggg ccagccagca
gaaacagtgg gctgtacaac atcaccttca aatatgacaa 300 ttgtaccacc
tacttgaatc cagtggggaa gcatgtgatt gctgacgccc agaatatcac 360
catcaggcag tatgcttgcc atgaccaagt ggcagtcacc attctttggt ccccaggggc
420 cctcggcatc gaattcctga aaggatttcg ggtaatactg gaggagctga
agtcggaggg 480 aagacagtgc caacaactga ttctaaagga tccgaagcag
ctcaacagta gcttcaaaag 540 aactggaatg gaatctcaac ctttcctgaa
tatgaaattt gaaacggatt atttcgtaaa 600 ggttgtccct tttccttcca
ttaaaaacga aagcaattac caccctttct tctttagaac 660 ccgagcctgt
gacctgttgt tacagccgga caatctagct tgtaaaccct tctggaagcc 720
tcggaacctg aacatcagcc agcatggctc ggacatgcag gtgtccttcg accacgcacc
780 gcacaacttc ggcttccgtt tcttctatct tcactacaag ctcaagcacg
aaggaccttt 840 caagcgaaag acctgtaagc aggagcaaac tacagagatg
accagctgcc tccttcaaaa 900 tgtttctcca ggggattata taattgagct
ggtggatgac actaacacaa caagaaaagt 960 gatgcattat gccttaaagc
cagtgcactc cccgtgggcc gggcccatca gagccgtggc 1020 catcacagtg
ccactggtag tcatatcggc attcgcgacg ctcttcactg tgatgtgccg 1080
caagaagcaa caagaaaata tatattcaca tttagatgaa gagagctctg agtcttccac
1140 atacactgca gcactcccaa gagagaggct ccggccgcgg ccgaaggtct
ttctctgcta 1200 ttccagtaaa gatggccaga atcacatgaa tgtcgtccag
tgtttcgcct acttcctcca 1260 ggacttctgt ggctgtgagg tggctctgga
cctgtgggaa gacttcagcc tctgtagaga 1320 agggcagaga gaatgggtca
tccagaagat ccacgagtcc cagttcatca ttgtggtttg 1380 ttccaaaggt
atgaagtact ttgtggacaa gaagaactac aaacacaaag gaggtggccg 1440
aggctcgggg aaaggagagc tcttcctggt ggcggtgtca gccattgccg aaaagctccg
1500 ccaggccaag cagagttcgt ccgcggcgct cagcaagttt atcgccgtct
actttgatta 1560 ttcctgcgag ggagacgtcc ccggtatcct agacctgagt
accaagtaca gactcatgga 1620 caatcttcct cagctctgtt cccacctgca
ctcccgagac cacggcctcc aggagccggg 1680 gcagcacacg cgacagggca
gcagaaggaa ctacttccgg agcaagtcag gccggtccct 1740 atacgtcgcc
atttgcaaca tgcaccagtt tattgacgag gagcccgact ggttcgaaaa 1800
gcagttcgtt cccttccatc ctcctccact gcgctaccgg gagccagtct tggagaaatt
1860 tgattcgggc ttggttttaa atgatgtcat gtgcaaacca gggcctgaga
gtgacttctg 1920 cctaaaggta gaggcggctg ttcttggggc aaccggacca
gccgactccc agcacgagag 1980 tcagcatggg ggcctggacc aagacgggga
ggcccggcct gcccttgacg gtagcgccgc 2040 cctgcaaccc ctgctgcaca
cggtgaaagc cggcagcccc tcggacatgc cgcgggactc 2100 aggcatctat
gactcgtctg tgccctcatc cgagctgtct ctgccactga tggaaggact 2160
ctcgacggac cagacagaaa cgtcttccct gacggagagc gtgtcctcct cttcaggcct
2220 gggtgaggag gaacctcctg cccttccttc caagctcctc tcttctgggt
catgcaaagc 2280 agatcttggt tgccgcagct acactgatga actccacgcg
gtcgcccctt tgtaacaaa 2339 8 234 DNA Homo sapiens 8 tgaagcgggc
agaaagagtg gtggatgatg tccggggact ggcatgaccc tgggtctcag 60
cagtgctgct tgcatttgga ctccatgggg ctttgtgttg gaagagcaaa ttggcttcac
120 tctgcatcat gttctcttgt tttcccacag ggagtggggc cagccagcag
aaacagtggg 180 ctgtacaaca tcaccttcaa atatgacaat tgtaccacct
acttgaatcc agtg 234 9 585 DNA Homo sapiens 9 gcggccgccg cggccaccgc
ccactcgggg ctggccagcg gcgggcggcc ggggcgcaga 60 gaacggcctg
gctgggcgag cgcacggcca tggccccgtg gctgcagctc tgctccgtct 120
tctttacggt caacgcctgc ctcaacggct cgcagctggc tgtggccgct ggcgggtccg
180 gccgcgcgcg gggcgccgac acctgtggct ggagggtaag gcgagggcgg
cgggtttctt 240 gccgtcgcca actcgcgggg aacgcagcgc gcacaggtgc
tcgcggggag gcgagcccgc 300 gccaacctgt ctgctcttcg cggggtccgc
ggccggcctg ggtctcactc ctcccgcgca 360 tcctcctggt ttccctcccc
ggacgcgtgt cctccggccc tggccgagat gaaagcggct 420 gcccgacccc
ggctttgtgt tgctaatgag ggagtggggc cagccagcag aaacagtggg 480
ctgtacaaca tcaccttcaa atatgacaat tgtaccacct acttgaatcc agtggggaag
540 catgtgattg ctgacgccca gaatatcacc atcagccagt atgct 585 10 2240
DNA Homo sapiens 10 gaggatcctg acggccatgg ccccgtggct gcagctctgc
tccgtcttct ttacggtcaa 60 cgcctgcctc aacggctcgc agctggctgt
ggccgctggc gggtccggcc gcgcgcgggg 120 cgccgacacc tgtggctgga
ggggagtggg gccagccagc agaaacagtg ggctgtacaa 180 catcaccttc
aaatatgaca attgtaccac ctacttgaat ccagtgggga agcatgtgat 240
tgctgacgcc cagaatatca
ccatcagcca gtatgcttgc catgaccaag tggcagtcac 300 cattctttgg
tccccagggg ccctcggcat cgaattcctg aaaggatttc gggtaatact 360
ggaggagctg aagtcggagg gaagacagtg ccaacaactg attctaaagg atccgaagca
420 gctcaacagt agcttcaaaa gaactggaat ggaatctcaa cctttcctga
atatgaaatt 480 tgaaacggat tatttcgtaa aggttgtccc ttttccttcc
attaaaaacg aaagcaatta 540 ccaccctttc ttctttagaa cccgagcctg
tgacctgttg ttacagccgg acaatctagc 600 ttgtaaaccc ttctggaagc
ctcggaacct gaacatcagc cagcatggct cggacatgca 660 ggtgtccttc
gaccacgcac cgcacaactt cggcttccgt ttcttctatc ttcactacaa 720
gctcaagcac gaaggacctt tcaagcgaaa gacctgtaag caggagcaaa ctacagagat
780 gaccagctgc ctccttcaaa atgtttctcc aggggattat ataattgagc
tggtggatga 840 cactaacaca acaagaaaag tgatgcatta tgccttaaag
ccagtgcact ccccgtgggc 900 cgggcccatc agagccgtgg ccatcacagt
gccactggta gtcatatcgg cattcgcgac 960 gctcttcact gtgatgtgcc
gcaagaagca acaagaaaat atatattcac atttagatga 1020 agagagctct
gagtcttcca catacactgc agcactccca agagagaggc tccggccgcg 1080
gccgaaggtc tttctctgct attccagtaa agatggccag aatcacatga atgtcgtcca
1140 gtgtttcgcc tacttcctcc aggacttctg tggctgtgag gtggctctgg
acctgtggga 1200 agacttcagc ctctgtagag aagggcagag agaatgggtc
atccagaaga tccacgagtc 1260 ccagttcatc attgtggttt gttccaaagg
catgaagtac tttgtggaca agaagaacta 1320 caaacacaaa ggaggtggcc
gaggctcggg gaaaggagag ctcttcctgg tggcggtgtc 1380 agccattgcc
gaaaagctcc gccaggccaa gcagagttcg tccgcggcgc tcagcaagtt 1440
tatcgccgtc tactttgatt attcctgcga gggagacgtc cccggtatcc tagacctgag
1500 taccaagtac agactcatgg acaatcttcc tcagctctgt tcccacctgc
actcccgaga 1560 ccacggcctc caggagccgg ggcagcacac gcgacagggc
agcagaagga actacttccg 1620 gagcaagtca ggccggtccc tatacgtcgc
catttgcaac atgcaccagt ttattgacga 1680 ggagcccgac tggttcgaaa
agcagttcgt tcccttccat cctcctccac tgcgctaccg 1740 ggagccagtc
ttggagaaat ttgattcggg cttggtttta aatgatgtca tgtgcaaacc 1800
agggcctgag agtgacttct gcctaaaggt agaggcggct gttcttgggg caaccggacc
1860 agccgactcc cagcacgaga gtcagcatgg gggcctggac caagacgggg
aggcccggcc 1920 tgcccttgac ggtagcgccg ccctgcaacc cctgctgcac
acggtgaaag ccggcagccc 1980 ctcggacatg ccgcgggact caggcatcta
tgactcgtct gtgccctcat ccgagctgtc 2040 tctgccactg atggaaggac
tctcgacgga ccagacagaa acgtcttccc tgacggagag 2100 cgtgtcctcc
tcttcaggcc tgggtgagga ggaacctcct gcccttcctt ccaagctcct 2160
ctcttctggg tcatgcaaag cagatcttgg ttgccgcagc tacactgatg aactccacgc
2220 ggtcgcccct ttgtaacaaa 2240 11 23 DNA Artificial sequence
Single strand DNA oligonucleotide 11 agcaagtcag gccggtccct ata 23
12 22 DNA Artificial sequence Single strand DNA oligonucleotide 12
ggtgaaggtc ggagtcaacg ga 22 13 22 DNA Artificial sequence Single
strand DNA oligonucleotide 13 gagggatctc gctcctggaa ga 22 14 115
PRT Artificial sequence Partial predicted amino acid sequence of
hSef-d 14 Ala Val Ala Asn Ser Arg Gly Thr Gln Arg Ala Gln Val Leu
Ala Gly 1 5 10 15 Arg Arg Ala Arg Ala Asn Leu Ser Ala Leu Arg Gly
Val Arg Gly Arg 20 25 30 Pro Gly Ser His Ser Ser Arg Ala Ser Ser
Trp Phe Pro Ser Pro Asp 35 40 45 Ala Cys Pro Pro Ala Leu Ala Glu
Met Lys Ala Ala Ala Arg Pro Arg 50 55 60 Leu Cys Val Ala Asn Glu
Gly Val Gly Pro Ala Ser Arg Asn Ser Gly 65 70 75 80 Leu Tyr Asn Ile
Thr Phe Lys Tyr Asp Asn Cys Thr Thr Tyr Leu Asn 85 90 95 Pro Val
Gly Lys His Val Ile Ala Asp Ala Gln Asn Ile Thr Ile Ser 100 105 110
Gln Tyr Ala 115 15 77 PRT Homo sapiens 15 Ser Gly Gln Lys Glu Trp
Trp Met Met Ser Gly Asp Trp His Asp Pro 1 5 10 15 Gly Ser Gln Gln
Cys Cys Leu His Leu Asp Ser Met Gly Leu Cys Val 20 25 30 Gly Arg
Ala Asn Trp Leu His Ser Ala Ser Cys Ser Leu Val Phe Pro 35 40 45
Gln Gly Val Gly Pro Ala Ser Arg Asn Ser Gly Leu Tyr Asn Ile Thr 50
55 60 Phe Lys Tyr Asp Asn Cys Thr Thr Tyr Leu Asn Pro Val 65 70 75
16 37 DNA Artificial sequence Single strand DNA oligonucleotide 16
gaggatcctg acggccatgg ccccgtggct gcagctc 37 17 24 DNA Artificial
sequence Single strand DNA oligonucleotide 17 tgaagctact gttgagctgc
ttcg 24 18 24 DNA Artificial sequence Single strand DNA
oligonucleotide 18 cagacgagtc atagatgcct gagt 24 19 25 DNA
Artificial sequence Single strand DNA oligonucleotide 19 cttcactctg
catcatgttc tcttg 25 20 23 DNA Artificial sequence Single strand DNA
oligonucleotide 20 gtgactgcca cttggtcatg gca 23 21 23 DNA
Artificial sequence Single strand DNA oligonucleotide 21 gacacctgtg
gctggagggt aag 23 22 60 DNA Artificial sequence hSef-b RACE derived
fragment 22 aaacgggaag tggccgtggg ccggtgaatt ccgtgtagtg gccaagcttt
gttccaaaga 60 23 19 DNA Artificial sequence ShRNA oligonucleotide
23 gtcggaggga agacagtgc 19 24 19 DNA Artificial sequence ShRNA
oligonucleotide 24 gcactgtctt ccctccgac 19 25 19 DNA Artificial
sequence ShRNA oligonucleotide 25 gcatgtgatt gctgacgcc 19 26 19 DNA
Artificial sequence ShRNA oligonucleotide 26 ggcgtcagca atcacatgc
19 27 19 DNA Artificial sequence ShRNA oligonucleotide 27
agcaggagca aactacaga 19 28 19 DNA Artificial sequence ShRNA
oligonucleotide 28 tctgtagttt gctcctgct 19 29 19 DNA Artificial
sequence ShRNA oligonucleotide 29 cgtgacagaa gggaggctg 19 30 19 DNA
Artificial sequence ShRNA oligonucleotide 30 cagcctccct tctgtcacg
19 31 613 DNA Artificial sequence In situ hybridization probe 31
acaaaggggc gaccgcgtgg agttcatcag tgtagctgcg gcaaccaaga tctgctttgc
60 atgacccaga agagaggagc ttggaaggaa gggcaggagg ttcctcctca
cccaggcctg 120 aagaggagga cacgctctcc gtcagggaag acgtttctgt
ctggtccgtc gagagtcctt 180 ccatcagtgg cagagacagc tcggatgagg
gcacagacga gtcatagatg cctgagtccc 240 gcggcatgtc cgaggggctg
ccggctttca ccgtgtgcag caggggttgc agggcggcgc 300 taccgtcaag
ggcaggccgg gcctccccgt cttggtccag gcccccatgc tgactctcgt 360
gctgggagtc ggctggtccg gttgccccaa gaacagccgc ctctaccttt aggcagaagt
420 cactctcagg ccctggtttg cacatgacat catttaaaac caagcccgaa
tcaaatttct 480 ccaagactgg ctcccggtag cgcagtggag gaggatggaa
gggaacgaac tgcttttcga 540 accagtcggg ctcctcgtca ataaactggt
gcatgttgca aatggcgacg tatagggacc 600 ggcctgactt gct 613
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References